Described herein is mask design and modeling for a set of masks to be successively imaged to print a composite pattern on a substrate, such as a semiconductor wafer. Further described herein is a method of double patterning a substrate with the set of masks. Also described herein is a method of correcting a drawn pattern of one of the mask levels based on a predicted pattern contour of the other of the mask levels. Also described herein is a method of modeling a resist profile contour for a mask level in which photoresist is applied onto a inhomogeneous substrate, as well as method of predicting a resist profile of a Boolean operation of two masks.