Abstract: A system which inspects pattern-bearing material that is subject to topical distortions which scans in a first direction a plurality of predefined local regions of a pattern to be inspected to provide an image of each local region and generates a reference image for each of the local regions. The system shifts the position of the image of each local region and the position of its corresponding reference image relative to each other to align the images in the second direction and/or modifies in the first direction the dimension of the image of each local region and the dimension of its corresponding reference image relative to each other to align the images in the first direction. For each local region the system compares the aligned images to detect errors in the pattern independent of misalignment of and topical distortions of each local region.