A method of inspecting a pattern on a substrate, by extracting boundary locations from design data for repeating blocks within the pattern, inspecting the substrate at only the boundary locations of the repeating blocks, detecting alignment errors at the boundary locations, comparing the alignment errors to a threshold, and flagging the alignment errors that exceed the threshold. In this manner, the alignment errors that were of no consequence in larger design rule devices can be detected, and a determination can be made as to whether they adversely impact the proper operation of the integrated circuit that will eventually be formed from the pattern. By performing the inspection only on the boundary locations, a much higher magnification can be used than what would be reasonably possible for an inspection of the entire substrate.