Some embodiments relate to a method of designing an integrated circuit layout. In this method, a plurality of design shapes are provided on different design layers over an active area within a graphical representation of the layout. A connection extends perpendicularly between a first design shape formed on a first design layer and a second design shape formed on the first design layer. First and second cut mask shapes on first and second cut mask design layers, respectively, are generated. The first cut shape removes portions of the first design layer and the second cut shape removes portions of the second design layer.