When the lengths of FEM wafers are automatically measured, not only the sizes of targets, the lengths of which are to be measured, are often varied from those in registration, but also the patterns of the targets are often deformed. Therefore, it is difficult to automatically determine whether the length measurement is possible or not. Therefore, the following are executed with a semiconductor inspection system: (1) a process of identifying the position of the contour line of an inspected image using a distance image calculated from a reference image, (2) a process of calculating a defect size image based on the position of the contour line with respect to the identified distance image, and detecting a defect candidate from the defect size image, and (3-1) a process of, upon detection of the defect candidate, calculating the size of the detected defect candidate, or (3-2) a process of detecting a portion different between the first and second contour lines as the defect candidate.