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diff --git a/bundles/org.simantics.modeling/src/org/simantics/modeling/migration/LayerCleanupMigrationStep.java b/bundles/org.simantics.modeling/src/org/simantics/modeling/migration/LayerCleanupMigrationStep.java
new file mode 100644
index 000000000..39c608709
--- /dev/null
+++ b/bundles/org.simantics.modeling/src/org/simantics/modeling/migration/LayerCleanupMigrationStep.java
@@ -0,0 +1,98 @@
+package org.simantics.modeling.migration;
+
+import java.util.List;
+
+import org.eclipse.core.runtime.IProgressMonitor;
+import org.simantics.db.Resource;
+import org.simantics.db.Session;
+import org.simantics.db.Statement;
+import org.simantics.db.WriteGraph;
+import org.simantics.db.common.CommentMetadata;
+import org.simantics.db.common.request.DelayedWriteRequest;
+import org.simantics.db.common.request.WriteRequest;
+import org.simantics.db.exception.DatabaseException;
+import org.simantics.db.layer0.migration.MigrationState;
+import org.simantics.db.layer0.migration.MigrationStep;
+import org.simantics.db.layer0.migration.MigrationUtils;
+import org.simantics.db.layer0.util.Layer0Utils;
+import org.simantics.db.layer0.util.RemoverUtil;
+import org.simantics.diagram.stubs.DiagramResource;
+import org.simantics.layer0.Layer0;
+import org.simantics.modeling.ModelingUtils;
+import org.simantics.utils.logging.TimeLogger;
+
+public class LayerCleanupMigrationStep implements MigrationStep {
+
+    @Override
+    public void applyTo(final IProgressMonitor monitor, Session session, MigrationState state) throws DatabaseException {
+    	
+	    TimeLogger.log("LayerCleanupMigrationStep");
+
+        final Resource indexRoot = MigrationUtils.getResource(monitor, session, state);
+        if(indexRoot == null) return;
+
+        monitor.setTaskName("Cleanup layers migration - remove layer assignments");
+
+        session.sync(new DelayedWriteRequest() {
+
+            @Override
+            public void perform(WriteGraph graph) throws DatabaseException {
+
+            	Layer0Utils.setDependenciesIndexingDisabled(graph, true);
+
+            	Layer0 L0 = Layer0.getInstance(graph);
+            	DiagramResource DIA = DiagramResource.getInstance(graph);
+
+            	for(Resource model : graph.getObjects(indexRoot, L0.ConsistsOf)) {
+            		
+            		List<Resource> elements = ModelingUtils.searchByType(graph, model, DIA.Element); 
+            		for(Resource element : Layer0Utils.sortByCluster(graph, elements)) {
+            			for(Statement stm : graph.getStatements(element, DIA.IsFocusable))
+            				graph.deny(stm);
+            			for(Statement stm : graph.getStatements(element, DIA.IsVisible))
+            				graph.deny(stm);
+            		}
+            		
+            	}
+            	
+            	CommentMetadata cm = graph.getMetadata(CommentMetadata.class);
+            	graph.addMetadata(cm.add("Removing deprecated layer assignments from the model."));
+            	
+            }
+            
+        });
+
+        monitor.setTaskName("Cleanup layers migration - remove layers");
+        
+        session.sync(new WriteRequest() {
+
+        	
+            @Override
+            public void perform(WriteGraph graph) throws DatabaseException {
+
+            	Layer0Utils.setDependenciesIndexingDisabled(graph, true);
+
+            	Layer0 L0 = Layer0.getInstance(graph);
+            	DiagramResource DIA = DiagramResource.getInstance(graph);
+
+            	for(Resource model : graph.getObjects(indexRoot, L0.ConsistsOf)) {
+            		
+            		for(Resource diagram : ModelingUtils.searchByType(graph, model, DIA.Composite)) {
+            			for(Resource layer : graph.getObjects(diagram, DIA.HasLayer))
+            				RemoverUtil.remove(graph, layer);
+            		}
+            		
+            	}
+            	
+            	CommentMetadata cm = graph.getMetadata(CommentMetadata.class);
+            	graph.addMetadata(cm.add("Removing deprecated layers from the model."));
+            	
+            }
+
+        });
+
+	    TimeLogger.log("LayerCleanupMigrationStep done");
+
+    }
+
+}