An inspection system determines, for each detected pattern defect, a defect inspection pattern area of predetermined dimensions containing the coordinates of the defect, then determines the clusters or cells whose reference points are located within the defect inspection pattern area. The system extracts the data of these clusters or cells from design pattern data read from a first magnetic disk unit. The system then generates an output file containing the extracted data. The output file is then converted into the same format as the input design pattern data or into OASIS format, before it is output to a second magnetic disk unit. The extracted pattern data specifying the clusters or cells within each defect inspection pattern area can be output from the mask inspection system to external systems.