diff --git a/src/db/db/dbDeepShapeStore.cc b/src/db/db/dbDeepShapeStore.cc
index 93c74ffba..bc9dc11d2 100644
--- a/src/db/db/dbDeepShapeStore.cc
+++ b/src/db/db/dbDeepShapeStore.cc
@@ -867,7 +867,9 @@ void DeepShapeStore::remove_ref (unsigned int layout, unsigned int layer)
 unsigned int
 DeepShapeStore::layout_for_iter (const db::RecursiveShapeIterator &si, const db::ICplxTrans &trans)
 {
-  layout_map_type::iterator l = m_layout_map.find (std::make_pair (si, trans));
+  size_t gen_id = si.layout () ? si.layout ()->hier_generation_id () : 0;
+
+  layout_map_type::iterator l = m_layout_map.find (std::make_pair (si, std::make_pair (gen_id, trans)));
   if (l == m_layout_map.end () || m_layouts[l->second] == 0) {
 
     unsigned int layout_index;
@@ -886,7 +888,7 @@ DeepShapeStore::layout_for_iter (const db::RecursiveShapeIterator &si, const db:
       layout.dbu (si.layout ()->dbu () / trans.mag ());
     }
 
-    m_layout_map[std::make_pair (si, trans)] = layout_index;
+    m_layout_map[std::make_pair (si, std::make_pair (gen_id, trans))] = layout_index;
     return layout_index;
 
   } else {
@@ -896,7 +898,8 @@ DeepShapeStore::layout_for_iter (const db::RecursiveShapeIterator &si, const db:
 
 void DeepShapeStore::make_layout (unsigned int layout_index, const db::RecursiveShapeIterator &si, const db::ICplxTrans &trans)
 {
-  tl_assert (m_layout_map.find (std::make_pair (si, trans)) == m_layout_map.end ());
+  size_t gen_id = si.layout () ? si.layout ()->hier_generation_id () : 0;
+  tl_assert (m_layout_map.find (std::make_pair (si, std::make_pair (gen_id, trans))) == m_layout_map.end ());
 
   while (m_layouts.size () <= layout_index) {
     m_layouts.push_back (0);
@@ -909,7 +912,7 @@ void DeepShapeStore::make_layout (unsigned int layout_index, const db::Recursive
     layout.dbu (si.layout ()->dbu () / trans.mag ());
   }
 
-  m_layout_map[std::make_pair (si, trans)] = layout_index;
+  m_layout_map[std::make_pair (si, std::make_pair (gen_id, trans))] = layout_index;
 }
 
 DeepLayer DeepShapeStore::create_polygon_layer (const db::RecursiveShapeIterator &si, double max_area_ratio, size_t max_vertex_count, const db::ICplxTrans &trans)
diff --git a/src/db/db/dbDeepShapeStore.h b/src/db/db/dbDeepShapeStore.h
index be6e838c0..1f12063b5 100644
--- a/src/db/db/dbDeepShapeStore.h
+++ b/src/db/db/dbDeepShapeStore.h
@@ -298,7 +298,7 @@ private:
 
 struct DB_PUBLIC RecursiveShapeIteratorCompareForTargetHierarchy
 {
-  bool operator () (const std::pair<db::RecursiveShapeIterator, db::ICplxTrans> &a, const std::pair<db::RecursiveShapeIterator, db::ICplxTrans> &b) const
+  bool operator () (const std::pair<db::RecursiveShapeIterator, std::pair<size_t, db::ICplxTrans> > &a, const std::pair<db::RecursiveShapeIterator, std::pair<size_t, db::ICplxTrans> > &b) const
   {
     int cmp_iter = db::compare_iterators_with_respect_to_target_hierarchy (a.first, b.first);
     if (cmp_iter != 0) {
@@ -865,7 +865,7 @@ private:
 
   void issue_variants (unsigned int layout, const std::map<db::cell_index_type, std::map<db::ICplxTrans, db::cell_index_type> > &var_map);
 
-  typedef std::map<std::pair<db::RecursiveShapeIterator, db::ICplxTrans>, unsigned int, RecursiveShapeIteratorCompareForTargetHierarchy> layout_map_type;
+  typedef std::map<std::pair<db::RecursiveShapeIterator, std::pair<size_t, db::ICplxTrans> >, unsigned int, RecursiveShapeIteratorCompareForTargetHierarchy> layout_map_type;
 
   //  no copying
   DeepShapeStore (const DeepShapeStore &);
diff --git a/src/drc/drc/built-in-macros/_drc_layer.rb b/src/drc/drc/built-in-macros/_drc_layer.rb
index dd6297364..e434c9d1d 100644
--- a/src/drc/drc/built-in-macros/_drc_layer.rb
+++ b/src/drc/drc/built-in-macros/_drc_layer.rb
@@ -5148,9 +5148,6 @@ CODE
 
       m = with_left ? "fill_with_left" : "fill"
 
-      # generation of new cells not tested in deep mode
-      @deep && raise("#{m} command not supported in deep mode currently")
-
       (@engine._output_layout && @engine._output_cell) || raise("#{m} command needs an output layout and output cell")
 
       source = @engine.source
diff --git a/src/drc/unit_tests/drcSimpleTests.cc b/src/drc/unit_tests/drcSimpleTests.cc
index 107aa58de..8b24c918d 100644
--- a/src/drc/unit_tests/drcSimpleTests.cc
+++ b/src/drc/unit_tests/drcSimpleTests.cc
@@ -1302,6 +1302,16 @@ TEST(47_fillWithOverlappingBoxesTiled)
   run_test (_this, "47", false);
 }
 
+TEST(47b_fillWithUsingOutput)
+{
+  run_test (_this, "47b", false);
+}
+
+TEST(47bd_fillWithUsingOutputDeep)
+{
+  run_test (_this, "47b", true);
+}
+
 TEST(48_drcWithFragments)
 {
   run_test (_this, "48", false);
diff --git a/testdata/drc/drcSimpleTests_47b.drc b/testdata/drc/drcSimpleTests_47b.drc
new file mode 100644
index 000000000..b20d4c81b
--- /dev/null
+++ b/testdata/drc/drcSimpleTests_47b.drc
@@ -0,0 +1,23 @@
+
+source $drc_test_source
+
+if $drc_test_deep
+  deep
+end
+
+to_fill = input(1, 0)
+
+# Create a fill pattern with a 0.025x0.025 µm box at 2/0
+pattern = fill_pattern("FILL_CELL").shape(2, 0, box(0, 0, 0.025, 0.025))
+
+# place every 25 nm
+to_fill.fill(pattern, hstep(0.025), vstep(0.025))
+
+# compute remaining parts
+l2 = input(2, 0)
+(to_fill - l2).output(100, 0)
+
+# we cannot use input(..) on the fill output if we use
+# a separate target layout, so wo do this:
+layout.layout.write($drc_test_target)
+
diff --git a/testdata/drc/drcSimpleTests_47b.gds b/testdata/drc/drcSimpleTests_47b.gds
new file mode 100644
index 000000000..89ba5d7df
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diff --git a/testdata/drc/drcSimpleTests_au47b.gds b/testdata/drc/drcSimpleTests_au47b.gds
new file mode 100644
index 000000000..d4dff937b
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diff --git a/testdata/drc/drcSimpleTests_au47bd.gds b/testdata/drc/drcSimpleTests_au47bd.gds
new file mode 100644
index 000000000..ba8325cc3
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