A method includes receiving data representing a layout of a DPT-layer of an integrated circuit generated by a place and route tool. The layout includes a plurality of polygons to be formed in the DPT-layer by a multi-patterning process. First and second ones of the plurality of polygons to be formed using first and second photomasks, respectively are identified. Any intervening polygons along a first path connecting the first polygon to the second polygon, and separator regions between adjacent polygons along the first path are identified. The separator regions have sizes less than a minimum threshold distance between polygons formed on the first photomask. The separator regions are counted. A multi-patterning conflict is identified, if the count of separator regions is even, prior to assigning all remaining ones of the plurality of polygons to the first or second masks.