diff --git a/masque/file/gdsii.py b/masque/file/gdsii.py
index 1b9c1d0..18fc9ff 100644
--- a/masque/file/gdsii.py
+++ b/masque/file/gdsii.py
@@ -28,7 +28,7 @@ import gdsii.library
 import gdsii.structure
 import gdsii.elements
 
-from .utils import mangle_name, make_dose_table, dose2dtype, dtype2dose
+from .utils import mangle_name, make_dose_table, dose2dtype, dtype2dose, clean_pattern_vertices
 from .. import Pattern, SubPattern, PatternError, Label, Shape
 from ..shapes import Polygon, Path
 from ..repetition import Grid
@@ -250,20 +250,10 @@ def read(stream: io.BufferedIOBase,
             # Switch based on element type:
             if isinstance(element, gdsii.elements.Boundary):
                 poly = _boundary_to_polygon(element, raw_mode)
-                if clean_vertices:
-                    try:
-                        poly.clean_vertices()
-                    except PatternError:
-                        continue
                 pat.shapes.append(poly)
 
             if isinstance(element, gdsii.elements.Path):
                 path = _gpath_to_mpath(element, raw_mode)
-                if clean_vertices:
-                    try:
-                        path.clean_vertices()
-                    except PatternError as err:
-                        continue
                 pat.shapes.append(path)
 
             elif isinstance(element, gdsii.elements.Text):
@@ -276,6 +266,8 @@ def read(stream: io.BufferedIOBase,
                   isinstance(element, gdsii.elements.ARef)):
                 pat.subpatterns.append(_ref_to_subpat(element))
 
+        if clean_vertices:
+            clean_pattern_vertices(pat)
         patterns.append(pat)
 
     # Create a dict of {pattern.name: pattern, ...}, then fix up all subpattern.pattern entries
diff --git a/masque/file/oasis.py b/masque/file/oasis.py
index 6e0284d..142b4a1 100644
--- a/masque/file/oasis.py
+++ b/masque/file/oasis.py
@@ -27,7 +27,7 @@ import fatamorgana
 import fatamorgana.records as fatrec
 from fatamorgana.basic import PathExtensionScheme, AString, NString, PropStringReference
 
-from .utils import mangle_name, make_dose_table
+from .utils import mangle_name, make_dose_table, clean_pattern_vertices
 from .. import Pattern, SubPattern, PatternError, Label, Shape
 from ..shapes import Polygon, Path, Circle
 from ..repetition import Grid, Arbitrary, Repetition
@@ -289,12 +289,6 @@ def read(stream: io.BufferedIOBase,
                                annotations=annotations,
                                repetition=repetition)
 
-                if clean_vertices:
-                    try:
-                        poly.clean_vertices()
-                    except PatternError:
-                        continue
-
                 pat.shapes.append(poly)
 
             elif isinstance(element, fatrec.Path):
@@ -321,12 +315,6 @@ def read(stream: io.BufferedIOBase,
                             cap=cap,
                             **path_args)
 
-                if clean_vertices:
-                    try:
-                        path.clean_vertices()
-                    except PatternError as err:
-                        continue
-
                 pat.shapes.append(path)
 
             elif isinstance(element, fatrec.Rectangle):
@@ -455,6 +443,8 @@ def read(stream: io.BufferedIOBase,
         for placement in cell.placements:
             pat.subpatterns.append(_placement_to_subpat(placement, lib))
 
+        if clean_vertices:
+            clean_pattern_vertices(pat)
         patterns.append(pat)
 
     # Create a dict of {pattern.name: pattern, ...}, then fix up all subpattern.pattern entries
diff --git a/masque/file/utils.py b/masque/file/utils.py
index e36765e..30b2808 100644
--- a/masque/file/utils.py
+++ b/masque/file/utils.py
@@ -6,6 +6,7 @@ import re
 import copy
 
 from .. import Pattern, PatternError
+from ..shapes import Polygon, Path
 
 
 def mangle_name(pattern: Pattern, dose_multiplier: float=1.0) -> str:
@@ -25,6 +26,30 @@ def mangle_name(pattern: Pattern, dose_multiplier: float=1.0) -> str:
     return sanitized_name
 
 
+def clean_pattern_vertices(pat: Pattern) -> Pattern:
+    """
+    Given a pattern, remove any redundant vertices in its polygons and paths.
+    The cleaning process completely removes any polygons with zero area or <3 vertices.
+
+    Args:
+        pat: Pattern to clean
+
+    Returns:
+        pat
+    """
+    remove_inds = []
+    for ii, shape in enumerate(pat.shapes):
+        if not isinstance(shape, (Polygon, Path)):
+            continue
+        try:
+            shape.clean_vertices()
+        except PatternError:
+            remove_inds.append(ii)
+    for ii in sorted(remove_inds, reverse=True):
+        del pat.shapes[ii]
+    return pat
+
+
 def make_dose_table(patterns: List[Pattern], dose_multiplier: float=1.0) -> Set[Tuple[int, float]]:
     """
     Create a set containing `(id(pat), written_dose)` for each pattern (including subpatterns)