Extra check to avoid a shapely warning when .intersects an empty shape

Author: momchil-flex

tidy3d/components/simulation.py

@@ -1837,7 +1837,7 @@ def _filter_structures_plane(  # pylint:disable=too-many-locals
                     continue
 
                 # look more closely to see if intersected.
-                if not shape.intersects(_shape):
+                if _shape.is_empty or not shape.intersects(_shape):
                     continue
 
                 diff_shape = _shape - shape