diff --git a/scripts/createScenarios.sh b/scripts/createScenarios.sh
index 514b77483336103494e6401d7951ecaba512b335..310d2b2ddcf3eee2f67390e4ef31df8e112d56c9 100755
--- a/scripts/createScenarios.sh
+++ b/scripts/createScenarios.sh
@@ -22,9 +22,15 @@ do
   if [ -z "$header" ]; then
      header=( "${array[@]}" )
   else
-     scenario="${array[0]}"
-     scenario_dir=$output_dir/$scenario
-     echo "$scenario in $scenario_dir"
+     ensemble="${array[0]}"
+     scenario="${array[1]}"
+     scenario_dir=$output_dir/$ensemble/$scenario
+     echo "$scenario for $ensemble in $scenario_dir"
+
+     if [ ! -d "$output_dir/$ensemble" ]; then
+        mkdir $output_dir/$ensemble
+     fi
+
      if [ ! -d "$scenario_dir" ]; then
         mkdir $scenario_dir
      elif [ $overwrite -ne 1 ]; then
diff --git a/scripts/scheduleScenarios.sh b/scripts/scheduleScenarios.sh
index 77aa5c435a3b51d3a6acfdef6b7581af612ba6e9..75065203d564b2a4aa6cdb67677f67bd049b901a 100755
--- a/scripts/scheduleScenarios.sh
+++ b/scripts/scheduleScenarios.sh
@@ -17,17 +17,18 @@ do
   if [ -z "$header" ]; then
      header=( "${array[@]}" )
   else
-     scenario="${array[0]}"
-     scenario_dir=$output_dir/$scenario
-     echo $scenario
+     ensemble="${array[0]}"
+     scenario="${array[1]}"
+     scenario_dir=$output_dir/$ensemble/$scenario
+     echo $scenario for $ensemble
 
      if [ ! -d "$scenario_dir" ]; then
         echo "Scenario $scenario dir is missing, so skipping"
         continue;
      fi
 
-     echo "qsub /exports/csce/eddie/geos/groups/LURG/models/PLUM/plumv2/scripts/runPlum.sh $scenario"
-     qsub /exports/csce/eddie/geos/groups/LURG/models/PLUM/plumv2/scripts/runPlum.sh $scenario
+     echo "qsub /exports/csce/eddie/geos/groups/LURG/models/PLUM/plumv2/scripts/runPlum.sh $ensemble/$scenario"
+     qsub /exports/csce/eddie/geos/groups/LURG/models/PLUM/plumv2/scripts/runPlum.sh $ensemble/$scenario
   fi
 done < $filename