Thanks for the response. As far as I can tell, there are 3 types of layers involved in cifinput. templayers, calma(GDS) layers, and the actual drawing layers that exist on a specific plane. In my previous example, isosub was created from SUBCUT and then subtracted dnwell. However, since isosub and dnwell are on the same plane. The initial creation of isosub from SUBCUT erased any existing dnwell. If I create drawing layers from templayers and calma layers, everything appears as expected. Sorry if my explanation was confusing.