An image of a mask pattern is overlaid on an image of a mask blank annotated with the center location and dimensions of each measured mask defect. Design clips centered at the measured defects are generated with lateral dimensions less than allowable movement of the mask pattern over the mask blank. Each design clip is converted into a binary image including pixels corresponding to defect-activating regions and pixels corresponding to defect-hiding regions. Each pixel region representing the defect-activating region is expanded by laterally biasing peripheries by one half of the lateral extent of the defect located within the corresponding design clip. Biased design clips are logically compiled pixel by pixel to determine an optimal pattern shift vector representing the amount of pattern shift.