diff --git a/docs/chapters/subcommands/setup.rst b/docs/chapters/subcommands/setup.rst
index a67c6571..96a927cc 100644
--- a/docs/chapters/subcommands/setup.rst
+++ b/docs/chapters/subcommands/setup.rst
@@ -14,7 +14,6 @@ Below is a list of available options that can be used with the ``setup`` command
 
   ishmael ~ # bastille setup -h
   Usage: bastille setup [option(s)] [bridge]
-                                    [filesystem]
                                     [loopback]
                                     [pf|firewall]
                                     [shared]
@@ -41,9 +40,6 @@ networking option. The ``loopback`` and ``shared`` options are only for cases wh
 is not specified during the ``create`` command. If an interface is specified, these options have no effect. 
 Instead, the specified interface will be used.
 
-The ``filesystem`` option is to ensure the proper datasets/directories are in place
-for using Bastille. This should only have to be run once on a new system.
-
 The ``shared`` option is for cases where you want an actual interface to use with bastille as
 opposed to a loopback. Jails will be linked to the shared interface on creation.
 
diff --git a/usr/local/share/bastille/bootstrap.sh b/usr/local/share/bastille/bootstrap.sh
index 062c79a1..4aff1089 100644
--- a/usr/local/share/bastille/bootstrap.sh
+++ b/usr/local/share/bastille/bootstrap.sh
@@ -81,7 +81,7 @@ bootstrap_directories() {
     if [ ! -d "${bastille_prefix}" ]; then
         if checkyesno bastille_zfs_enable; then
             if [ -n "${bastille_zfs_zpool}" ]; then
-                zfs create ${bastille_zfs_options} -o mountpoint="${bastille_prefix}" "${bastille_zfs_zpool}/${bastille_zfs_prefix}"
+                zfs create ${bastille_zfs_options} -o mountpoint="${bastille_prefix_mountpoint}" "${bastille_zfs_zpool}/${bastille_zfs_prefix}"
             fi
         else
             mkdir -p "${bastille_prefix}"
@@ -90,9 +90,9 @@ bootstrap_directories() {
     # Make sure the dataset is mounted in the proper place
     elif [ -d "${bastille_prefix}" ] && checkyesno bastille_zfs_enable; then
         if ! zfs list "${bastille_zfs_zpool}/${bastille_zfs_prefix}" >/dev/null; then
-            zfs create ${bastille_zfs_options} -o mountpoint="${bastille_prefix}" "${bastille_zfs_zpool}/${bastille_zfs_prefix}"
+            zfs create ${bastille_zfs_options} -o mountpoint="${bastille_prefix_mountpoint}" "${bastille_zfs_zpool}/${bastille_zfs_prefix}"
         elif [ "$(zfs get -H -o value mountpoint ${bastille_zfs_zpool}/${bastille_zfs_prefix})" != "${bastille_prefix}" ]; then
-            zfs set mountpoint="${bastille_prefix}" "${bastille_zfs_zpool}/${bastille_zfs_prefix}"
+            zfs set mountpoint="${bastille_prefix_mountpoint}" "${bastille_zfs_zpool}/${bastille_zfs_prefix}"
         fi
     fi
 
@@ -100,7 +100,7 @@ bootstrap_directories() {
     if [ ! -d "${bastille_backupsdir}" ]; then
         if checkyesno bastille_zfs_enable; then
             if [ -n "${bastille_zfs_zpool}" ]; then
-                zfs create ${bastille_zfs_options} -o mountpoint="${bastille_backupsdir}" "${bastille_zfs_zpool}/${bastille_zfs_prefix}/backups"
+                zfs create ${bastille_zfs_options} -o mountpoint="${bastille_backupsdir_mountpoint}" "${bastille_zfs_zpool}/${bastille_zfs_prefix}/backups"
             fi
         else
             mkdir -p "${bastille_backupsdir}"
@@ -112,10 +112,10 @@ bootstrap_directories() {
     if [ ! -d "${bastille_cachedir}" ]; then
         if checkyesno bastille_zfs_enable; then
             if [ -n "${bastille_zfs_zpool}" ]; then
-                zfs create ${bastille_zfs_options} -o mountpoint="${bastille_cachedir}" "${bastille_zfs_zpool}/${bastille_zfs_prefix}/cache"
+                zfs create ${bastille_zfs_options} -o mountpoint="${bastille_cachedir_mountpoint}" "${bastille_zfs_zpool}/${bastille_zfs_prefix}/cache"
                 # Don't create unused/stale cache/RELEASE directory on Linux jails creation.
                 if [ -z "${NOCACHEDIR}" ]; then
-                    zfs create ${bastille_zfs_options} -o mountpoint="${bastille_cachedir}/${RELEASE}" "${bastille_zfs_zpool}/${bastille_zfs_prefix}/cache/${RELEASE}"
+                    zfs create ${bastille_zfs_options} -o mountpoint="${bastille_cachedir_mountpoint}/${RELEASE}" "${bastille_zfs_zpool}/${bastille_zfs_prefix}/cache/${RELEASE}"
                 fi
             fi
         else
@@ -131,7 +131,7 @@ bootstrap_directories() {
         if [ -z "${NOCACHEDIR}" ]; then
             if checkyesno bastille_zfs_enable; then
                 if [ -n "${bastille_zfs_zpool}" ]; then
-                    zfs create ${bastille_zfs_options} -o mountpoint="${bastille_cachedir}/${RELEASE}" "${bastille_zfs_zpool}/${bastille_zfs_prefix}/cache/${RELEASE}"
+                    zfs create ${bastille_zfs_options} -o mountpoint="${bastille_cachedir_mountpoint}/${RELEASE}" "${bastille_zfs_zpool}/${bastille_zfs_prefix}/cache/${RELEASE}"
                 fi
             else
                 mkdir -p "${bastille_cachedir}/${RELEASE}"
@@ -143,7 +143,7 @@ bootstrap_directories() {
     if [ ! -d "${bastille_jailsdir}" ]; then
         if checkyesno bastille_zfs_enable; then
             if [ -n "${bastille_zfs_zpool}" ]; then
-                zfs create ${bastille_zfs_options} -o mountpoint="${bastille_jailsdir}" "${bastille_zfs_zpool}/${bastille_zfs_prefix}/jails"
+                zfs create ${bastille_zfs_options} -o mountpoint="${bastille_jailsdir_mountpoint}" "${bastille_zfs_zpool}/${bastille_zfs_prefix}/jails"
             fi
         else
             mkdir -p "${bastille_jailsdir}"
@@ -154,7 +154,7 @@ bootstrap_directories() {
     if [ ! -d "${bastille_logsdir}" ]; then
         if checkyesno bastille_zfs_enable; then
             if [ -n "${bastille_zfs_zpool}" ]; then
-                zfs create ${bastille_zfs_options} -o mountpoint="${bastille_logsdir}" "${bastille_zfs_zpool}/${bastille_zfs_prefix}/logs"
+                zfs create ${bastille_zfs_options} -o mountpoint="${bastille_logsdir_mountpoint}" "${bastille_zfs_zpool}/${bastille_zfs_prefix}/logs"
             fi
         else
             mkdir -p "${bastille_logsdir}"
@@ -165,7 +165,7 @@ bootstrap_directories() {
     if [ ! -d "${bastille_templatesdir}" ]; then
         if checkyesno bastille_zfs_enable; then
             if [ -n "${bastille_zfs_zpool}" ]; then
-                zfs create ${bastille_zfs_options} -o mountpoint="${bastille_templatesdir}" "${bastille_zfs_zpool}/${bastille_zfs_prefix}/templates"
+                zfs create ${bastille_zfs_options} -o mountpoint="${bastille_templatesdir_mountpoint}" "${bastille_zfs_zpool}/${bastille_zfs_prefix}/templates"
             fi
         else
             mkdir -p "${bastille_templatesdir}"
@@ -176,8 +176,8 @@ bootstrap_directories() {
     if [ ! -d "${bastille_releasesdir}" ]; then
         if checkyesno bastille_zfs_enable; then
             if [ -n "${bastille_zfs_zpool}" ]; then
-                zfs create ${bastille_zfs_options} -o mountpoint="${bastille_releasesdir}" "${bastille_zfs_zpool}/${bastille_zfs_prefix}/releases"
-                zfs create ${bastille_zfs_options} -o mountpoint="${bastille_releasesdir}/${RELEASE}" "${bastille_zfs_zpool}/${bastille_zfs_prefix}/releases/${RELEASE}"
+                zfs create ${bastille_zfs_options} -o mountpoint="${bastille_releasesdir_mountpoint}" "${bastille_zfs_zpool}/${bastille_zfs_prefix}/releases"
+                zfs create ${bastille_zfs_options} -o mountpoint="${bastille_releasesdir_mountpoint}/${RELEASE}" "${bastille_zfs_zpool}/${bastille_zfs_prefix}/releases/${RELEASE}"
             fi
         else
             mkdir -p "${bastille_releasesdir}/${RELEASE}"
@@ -186,7 +186,7 @@ bootstrap_directories() {
     elif [ ! -d "${bastille_releasesdir}/${RELEASE}" ]; then
         if checkyesno bastille_zfs_enable; then
             if [ -n "${bastille_zfs_zpool}" ]; then
-                zfs create ${bastille_zfs_options} -o mountpoint="${bastille_releasesdir}/${RELEASE}" "${bastille_zfs_zpool}/${bastille_zfs_prefix}/releases/${RELEASE}"
+                zfs create ${bastille_zfs_options} -o mountpoint="${bastille_releasesdir_mountpoint}/${RELEASE}" "${bastille_zfs_zpool}/${bastille_zfs_prefix}/releases/${RELEASE}"
             fi
        else
            mkdir -p "${bastille_releasesdir}/${RELEASE}"
diff --git a/usr/local/share/bastille/common.sh b/usr/local/share/bastille/common.sh
index 3ba0c84e..467103f6 100644
--- a/usr/local/share/bastille/common.sh
+++ b/usr/local/share/bastille/common.sh
@@ -295,6 +295,34 @@ set_target_single() {
     export JAILS
 }
 
+set_zfs_mountpoints() {
+
+    # We have to do this if ALTROOT is enabled/present
+    local _altroot="$(zpool get -Ho value altroot ${bastille_zfs_zpool})"
+
+    if [ "${_altroot}" != "-" ]; then
+
+        # Set mountpoints to *dir*
+        bastille_prefix_mountpoint="${bastille_prefix}"
+        bastille_backupsdir_mountpoint="${bastille_backupsdir}"
+        bastille_cachedir_mountpoint="${bastille_cachedir}"
+        bastille_jailsdir_mountpoint="${bastille_jailsdir}"
+        bastille_releasesdir_mountpoint="${bastille_releasesdir}"
+        bastille_templatesdir_mountpoint="${bastille_templatesdir}"
+        bastille_logsdir_mountpoint="${bastille_logsdir}"  
+
+        # Set *dir* to include ALTROOT
+        bastille_prefix="${_altroot}${bastille_prefix}"
+        bastille_backupsdir="${_altroot}${bastille_backupsdir}"
+        bastille_cachedir="${_altroot}${bastille_cachedir}"
+        bastille_jailsdir="${_altroot}${bastille_jailsdir}"
+        bastille_releasesdir="${_altroot}${bastille_releasesdir}"
+        bastille_templatesdir="${_altroot}${bastille_templatesdir}"
+        bastille_logsdir="${_altroot}${bastille_logsdir}" 
+
+    fi
+}
+
 target_all_jails() {
     local _JAILS="$(bastille list jails)"
     JAILS=""
@@ -504,4 +532,4 @@ checkyesno() {
         return 1
         ;;
     esac
-}
+}
\ No newline at end of file
diff --git a/usr/local/share/bastille/import.sh b/usr/local/share/bastille/import.sh
index 9d004840..ce6d795f 100644
--- a/usr/local/share/bastille/import.sh
+++ b/usr/local/share/bastille/import.sh
@@ -137,12 +137,13 @@ validate_archive() {
 }
 
 update_zfsmount() {
+	
     # Update the mountpoint property on the received ZFS data stream
     OLD_ZFS_MOUNTPOINT=$(zfs get -H mountpoint "${bastille_zfs_zpool}/${bastille_zfs_prefix}/jails/${TARGET_TRIM}/root" | awk '{print $3}')
     NEW_ZFS_MOUNTPOINT="${bastille_jailsdir}/${TARGET_TRIM}/root"
     if [ "${NEW_ZFS_MOUNTPOINT}" != "${OLD_ZFS_MOUNTPOINT}" ]; then
         info "\nUpdating ZFS mountpoint..."
-        zfs set mountpoint="${bastille_jailsdir}/${TARGET_TRIM}/root" "${bastille_zfs_zpool}/${bastille_zfs_prefix}/jails/${TARGET_TRIM}/root"
+        zfs set mountpoint="${bastille_jailsdir_mountpoint}/${TARGET_TRIM}/root" "${bastille_zfs_zpool}/${bastille_zfs_prefix}/jails/${TARGET_TRIM}/root"
     fi
 
     # Mount new container ZFS datasets
diff --git a/usr/local/share/bastille/setup.sh b/usr/local/share/bastille/setup.sh
index 5bf8fb1e..7bcd84dc 100644
--- a/usr/local/share/bastille/setup.sh
+++ b/usr/local/share/bastille/setup.sh
@@ -34,7 +34,6 @@
 
 usage() {
     error_notify "Usage: bastille setup [option(s)] [bridge]"
-    error_notify "                                  [filesystem]"
     error_notify "                                  [loopback]"
     error_notify "                                  [pf|firewall]"
     error_notify "                                  [shared]"
@@ -91,98 +90,6 @@ OPT_CONFIG="${1}"
 
 bastille_root_check
 
-configure_filesystem() {
-
-    # This is so we dont have to introduce breaking
-    # changes on new variables added to bastille.conf
-
-    ## ${bastille_prefix}
-    if [ ! -d "${bastille_prefix}" ]; then
-        if checkyesno bastille_zfs_enable; then
-            if [ -n "${bastille_zfs_zpool}" ]; then
-                zfs create ${bastille_zfs_options} -o mountpoint="${bastille_prefix}" "${bastille_zfs_zpool}/${bastille_zfs_prefix}"
-            fi
-        else
-            mkdir -p "${bastille_prefix}"
-        fi
-        chmod 0750 "${bastille_prefix}"
-    # Make sure the dataset is mounted in the proper place
-    elif [ -d "${bastille_prefix}" ] && checkyesno bastille_zfs_enable; then
-        if ! zfs list "${bastille_zfs_zpool}/${bastille_zfs_prefix}" >/dev/null; then
-            zfs create ${bastille_zfs_options} -o mountpoint="${bastille_prefix}" "${bastille_zfs_zpool}/${bastille_zfs_prefix}"
-        elif [ "$(zfs get -H -o value mountpoint ${bastille_zfs_zpool}/${bastille_zfs_prefix})" != "${bastille_prefix}" ]; then
-            zfs set mountpoint="${bastille_prefix}" "${bastille_zfs_zpool}/${bastille_zfs_prefix}"
-        fi
-    fi
-
-    ## ${bastille_backupsdir}
-    if [ ! -d "${bastille_backupsdir}" ]; then
-        if checkyesno bastille_zfs_enable; then
-            if [ -n "${bastille_zfs_zpool}" ]; then
-                zfs create ${bastille_zfs_options} -o mountpoint="${bastille_backupsdir}" "${bastille_zfs_zpool}/${bastille_zfs_prefix}/backups"
-            fi
-        else
-            mkdir -p "${bastille_backupsdir}"
-        fi
-        chmod 0750 "${bastille_backupsdir}"
-    fi
-
-    ## ${bastille_cachedir}
-    if [ ! -d "${bastille_cachedir}" ]; then
-        if checkyesno bastille_zfs_enable; then
-            if [ -n "${bastille_zfs_zpool}" ]; then
-                zfs create ${bastille_zfs_options} -o mountpoint="${bastille_cachedir}" "${bastille_zfs_zpool}/${bastille_zfs_prefix}/cache"
-            fi
-        else
-            mkdir -p "${bastille_cachedir}"
-        fi
-    fi
-
-    ## ${bastille_jailsdir}
-    if [ ! -d "${bastille_jailsdir}" ]; then
-        if checkyesno bastille_zfs_enable; then
-            if [ -n "${bastille_zfs_zpool}" ]; then
-                zfs create ${bastille_zfs_options} -o mountpoint="${bastille_jailsdir}" "${bastille_zfs_zpool}/${bastille_zfs_prefix}/jails"
-            fi
-        else
-            mkdir -p "${bastille_jailsdir}"
-        fi
-    fi
-
-    ## ${bastille_logsdir}
-    if [ ! -d "${bastille_logsdir}" ]; then
-        if checkyesno bastille_zfs_enable; then
-            if [ -n "${bastille_zfs_zpool}" ]; then
-                zfs create ${bastille_zfs_options} -o mountpoint="${bastille_logsdir}" "${bastille_zfs_zpool}/${bastille_zfs_prefix}/logs"
-            fi
-        else
-            mkdir -p "${bastille_logsdir}"
-        fi
-    fi
-
-    ## ${bastille_templatesdir}
-    if [ ! -d "${bastille_templatesdir}" ]; then
-        if checkyesno bastille_zfs_enable; then
-            if [ -n "${bastille_zfs_zpool}" ]; then
-                zfs create ${bastille_zfs_options} -o mountpoint="${bastille_templatesdir}" "${bastille_zfs_zpool}/${bastille_zfs_prefix}/templates"
-            fi
-        else
-            mkdir -p "${bastille_templatesdir}"
-        fi
-    fi
-
-    ## ${bastille_releasesdir}
-    if [ ! -d "${bastille_releasesdir}" ]; then
-        if checkyesno bastille_zfs_enable; then
-            if [ -n "${bastille_zfs_zpool}" ]; then
-                zfs create ${bastille_zfs_options} -o mountpoint="${bastille_releasesdir}" "${bastille_zfs_zpool}/${bastille_zfs_prefix}/releases"
-            fi
-        else
-            mkdir -p "${bastille_releasesdir}"
-        fi
-    fi
-}
-
 # Configure netgraph
 configure_netgraph() {
     if [ ! "$(kldstat -m netgraph)" ]; then
@@ -389,7 +296,6 @@ configure_storage() {
 # Run all base functions (w/o vnet) if no args
 if [ $# -eq 0 ]; then
     sysrc bastille_enable=YES
-    configure_filesystem
     configure_storage
     configure_loopback_interface
     configure_pf
@@ -398,9 +304,6 @@ if [ $# -eq 0 ]; then
 fi
 
 case "${OPT_CONFIG}" in
-    filesystem)
-        configure_filesystem
-        ;;
     pf|firewall)
         configure_pf
         ;;