diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java
index 30baa1a2231359e2882fb776fbf680e2a8ef0748..56278534534733f14cd829988410ef5650b393c6 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java
@@ -136,15 +136,6 @@ public class CreateHierarchyCommand extends ModelCommand {
         alias.setTransparencyLevel("");
       }
     }
-    Set<Compartment> toRemove = new HashSet<>();
-    for (final Compartment alias : getModel().getCompartments()) {
-      if (alias instanceof PathwayCompartment) {
-        toRemove.add(alias);
-      }
-    }
-    for (final Compartment alias : toRemove) {
-      getModel().removeElement(alias);
-    }
   }
 
   /**