diff --git a/src/com/xilinx/rapidwright/edif/EDIFNetlist.java b/src/com/xilinx/rapidwright/edif/EDIFNetlist.java
index 601f0f3dc..dd00e981e 100644
--- a/src/com/xilinx/rapidwright/edif/EDIFNetlist.java
+++ b/src/com/xilinx/rapidwright/edif/EDIFNetlist.java
@@ -481,26 +481,41 @@ public List<String> getComments() {
     }
 
     /**
-     * Migrates all cells in the provided library
-     * into the standard work library.
-     * @param library The library with cells to be migrated to work.
+     * Migrates all cells in the provided library into the standard work library.
+     * 
+     * @param library          The library with cells to be migrated to work.
+     * @param renameCollisions Flag to rename cells upon name collision
      */
-    public void migrateToWorkLibrary(String library) {
+    public void migrateToWorkLibrary(String library, boolean renameCollisions) {
         EDIFLibrary work = getWorkLibrary();
         EDIFLibrary oldWork = getLibrary(library);
         List<EDIFCell> toRemove = new ArrayList<>(oldWork.getCells());
         for (EDIFCell c : toRemove) {
             oldWork.removeCell(c);
-            work.addCell(c);
+            if (renameCollisions) {
+                work.addCellRenameDuplicates(c, "Work");
+            } else {
+                work.addCell(c);
+            }
         }
         removeLibrary(library);
     }
 
     /**
-     * Migrates all libraries except HDI primitives and work to
-     * the work library.
+     * Migrates all cells in the provided library into the standard work library.
+     * 
+     * @param library The library with cells to be migrated to work.
      */
-    public void consolidateAllToWorkLibrary() {
+    public void migrateToWorkLibrary(String library) {
+        migrateToWorkLibrary(library, false);
+    }
+
+    /**
+     * Migrates all libraries except HDI primitives and work to the work library.
+     * 
+     * @param renameCollisions Flag to rename cells upon name collision
+     */
+    public void consolidateAllToWorkLibrary(boolean renameCollisions) {
         List<EDIFLibrary> librariesToMigrate = new ArrayList<>();
         for (EDIFLibrary l : getLibraries()) {
             if (!l.isHDIPrimitivesLibrary() && !l.isWorkLibrary()) {
@@ -508,10 +523,17 @@ public void consolidateAllToWorkLibrary() {
             }
         }
         for (EDIFLibrary l : librariesToMigrate) {
-            migrateToWorkLibrary(l.getName());
+            migrateToWorkLibrary(l.getName(), renameCollisions);
         }
     }
 
+    /**
+     * Migrates all libraries except HDI primitives and work to the work library.
+     */
+    public void consolidateAllToWorkLibrary() {
+        consolidateAllToWorkLibrary(false);
+    }
+
     private EDIFCell migrateCellAndSubCellsWorker(EDIFCell cell) {
         EDIFLibrary srcLib = cell.getLibrary();
         EDIFLibrary destLib = getLibrary(srcLib.getName());
diff --git a/src/com/xilinx/rapidwright/ipi/BlockStitcher.java b/src/com/xilinx/rapidwright/ipi/BlockStitcher.java
index 2d84eaf58..0b7de6d52 100644
--- a/src/com/xilinx/rapidwright/ipi/BlockStitcher.java
+++ b/src/com/xilinx/rapidwright/ipi/BlockStitcher.java
@@ -107,16 +107,17 @@ public class BlockStitcher {
     private ArrayList<EDIFHierPortInst> getPassThruPortInsts(Port port, EDIFHierPortInst curr) {
         ArrayList<EDIFHierPortInst> list = new ArrayList<>();
         for (String name : port.getPassThruPortNames()) {
-            EDIFPortInst passThruInst = curr.getPortInst().getCellInst().getPortInst(name);
+            EDIFHierCellInst hierInst = curr.getHierarchicalInst();
+            EDIFPortInst passThruInst = hierInst.getInst().getPortInst(name);
             if (passThruInst == null) {
-                String unconnected = curr.getPortInst().getCellInst().getName() + EDIFTools.EDIF_HIER_SEP + name;
+                String unconnected = hierInst.getInst().getName() + EDIFTools.EDIF_HIER_SEP + name;
                 if (!reportedUnconnects.contains(unconnected)) {
                     System.out.println("INFO: Port " + unconnected + " is unconnected");
                     reportedUnconnects.add(unconnected);
                 }
                 continue;
             }
-            EDIFHierPortInst passThru = new EDIFHierPortInst(curr.getHierarchicalInst(), passThruInst);
+            EDIFHierPortInst passThru = new EDIFHierPortInst(hierInst.getParent(), passThruInst);
             list.add(passThru);
         }
         return list;
@@ -462,7 +463,7 @@ public static void main(String[] args) {
         }
         t.stop().start("Reading Top Level EDIF");
         EDIFNetlist topEdifNetlist = EDIFTools.readEdifFile(args[1]);
-        Design stitched = new Design("top_stitched", stitcher.partName);
+        Design stitched = new Design(topEdifNetlist.getName(), stitcher.partName);
         stitched.setNetlist(topEdifNetlist);
         t.stop().start("Implement Blocks");
         stitcher.populateModuleInstMaps(topEdifNetlist);
@@ -534,7 +535,7 @@ public static void main(String[] args) {
             }
             //System.out.println(modInstName + " " + implementationIndex);
             EDIFNetlist tmp = stitched.getNetlist();
-            stitched.setNetlist(null);
+            stitched.setNetlist(EDIFTools.createNewNetlist("dummy"));
             ModuleInst mi = stitched.createModuleInst(modInstName, modImpls.get(implementationIndex));
             stitched.setNetlist(tmp);
             miMap.put(mi, modImpls.getNetlist());
@@ -590,18 +591,19 @@ public static void main(String[] args) {
             inst.setCellType(cellType);
         }
 
-        for (EDIFCell c : stitched.getNetlist().getLibrary("IP_Integrator_Lib").getCells()) {
-            work.addCell(c);
-        }
-
-        ArrayList<String> libsToRemove = new ArrayList<>();
-        for (EDIFLibrary lib : stitched.getNetlist().getLibraries()) {
-            if (lib.getName().equals(EDIFTools.EDIF_LIBRARY_HDI_PRIMITIVES_NAME) ||
-                    lib.getName().equals(EDIFTools.EDIF_LIBRARY_WORK_NAME)) continue;
-            libsToRemove.add(lib.getName());
-        }
-        for (String lib : libsToRemove) {
-            stitched.getNetlist().removeLibrary(lib);
+        // Move all cells to 'work' library
+        boolean renameCollisions = true;
+        stitched.getNetlist().consolidateAllToWorkLibrary(renameCollisions);
+        EDIFLibrary workLib = stitched.getNetlist().getWorkLibrary();
+        for (EDIFCell workCell : workLib.getCells()) {
+            for (EDIFCellInst inst : workCell.getCellInsts()) {
+                EDIFLibrary lib = inst.getCellType().getLibrary();
+                if (lib.isHDIPrimitivesLibrary() || lib == workLib) {
+                    continue;
+                } else {
+                    inst.setCellType(work.getCell(inst.getCellType().getName()));
+                }
+            }
         }
         t.stop();
         if (DUMP_SYNTH_DCP_ONLY) {