diff --git a/masque/builder/tools.py b/masque/builder/tools.py
index 1db156b..6a58b70 100644
--- a/masque/builder/tools.py
+++ b/masque/builder/tools.py
@@ -378,7 +378,7 @@ class SimpleTool(Tool, metaclass=ABCMeta):
             else:
                 straight_tree = straight_pat_or_tree
                 top = straight_tree.top()
-                straight_tree.flatten(top)
+                straight_tree.flatten(top, dangling_ok=True)
                 pat.plug(straight_tree[top], pmap, append=True)
         if data.ccw is not None:
             bend, bport_in, bport_out = self.bend
@@ -653,7 +653,7 @@ class AutoTool(Tool, metaclass=ABCMeta):
             else:
                 straight_tree = straight_pat_or_tree
                 top = straight_tree.top()
-                straight_tree.flatten(top)
+                straight_tree.flatten(top, dangling_ok=True)
                 pat.plug(straight_tree[top], pmap, append=True)
         if data.b_transition:
             pat.plug(data.b_transition.abstract, {port_names[1]: data.b_transition.our_port_name})
@@ -801,7 +801,7 @@ class AutoTool(Tool, metaclass=ABCMeta):
             else:
                 straight_tree = straight_pat_or_tree
                 top = straight_tree.top()
-                straight_tree.flatten(top)
+                straight_tree.flatten(top, dangling_ok=True)
                 pat.plug(straight_tree[top], pmap, append=True)
         if data.b_transition:
             pat.plug(data.b_transition.abstract, {port_names[1]: data.b_transition.our_port_name})
@@ -813,7 +813,7 @@ class AutoTool(Tool, metaclass=ABCMeta):
             else:
                 sbend_tree = sbend_pat_or_tree
                 top = sbend_tree.top()
-                sbend_tree.flatten(top)
+                sbend_tree.flatten(top, dangling_ok=True)
                 pat.plug(sbend_tree[top], pmap, append=True, mirrored=data.jog_remaining < 0)
         if data.out_transition:
             pat.plug(data.out_transition.abstract, {port_names[1]: data.out_transition.our_port_name})
diff --git a/masque/library.py b/masque/library.py
index b52da74..9e7c133 100644
--- a/masque/library.py
+++ b/masque/library.py
@@ -264,6 +264,7 @@ class ILibraryView(Mapping[str, 'Pattern'], metaclass=ABCMeta):
             self,
             tops: str | Sequence[str],
             flatten_ports: bool = False,
+            dangling_ok: bool = False,
             ) -> dict[str, 'Pattern']:
         """
         Returns copies of all `tops` patterns with all refs
@@ -276,6 +277,9 @@ class ILibraryView(Mapping[str, 'Pattern'], metaclass=ABCMeta):
             tops: The pattern(s) to flattern.
             flatten_ports: If `True`, keep ports from any referenced
                 patterns; otherwise discard them.
+            dangling_ok: If `True`, no error will be thrown if any
+                ref points to a name which is not present in the library.
+                Default False.
 
         Returns:
             {name: flat_pattern} mapping for all flattened patterns.
@@ -292,6 +296,8 @@ class ILibraryView(Mapping[str, 'Pattern'], metaclass=ABCMeta):
             for target in pat.refs:
                 if target is None:
                     continue
+                if dangling_ok and target not in self:
+                    continue
                 if target not in flattened:
                     flatten_single(target)
 
@@ -307,7 +313,9 @@ class ILibraryView(Mapping[str, 'Pattern'], metaclass=ABCMeta):
                         p.ports.clear()
                     pat.append(p)
 
-            pat.refs.clear()
+            for target in set(pat.refs.keys()) & set(self.keys()):
+                del pat.refs[target]
+
             flattened[name] = pat
 
         for top in tops: