A method and system is disclosed for inspecting defects on a wafer. After acquiring at least one digitized image of at least one portion of a wafer, at least one design database file corresponding to the portion of the wafer is converted into at least one inspection file. After setting one or more error detection thresholds, the digitized image and the inspection file are compared by an inspection tool for detecting defects with regard to the portion of the wafer based on the set error detection thresholds.