Abstract: Method and system for performing semiconductor manufacturing scratch recognition analysis in cooperation with wafer scanning tools is disclosed. The invention comprises a method for determining from scan data associated with defects or other points on a substrate, such as a semiconductor wafer, what defects comprise part of a scratch. The method comprises, for each cluster of defects, determining whether the cluster includes a minimum number of pixels, or defects. For each cluster comprising the minimum number of defects, determining the best fit line for the cluster, rotating the best fit line about its center of gravity to "fine tune" the fitness thereof, and then calculating the line attributes of the fine tuned best fit line to determine whether the cluster is a scratch and classifying the cluster accordingly.