Abstract: A method of locating and characterizing defects on semiconductor using a scanner device and a high-magnification imaging device comprises the steps of scanning (A) a test wafer a plurality of times with the scanner device, recording the scanner device coordinates of defects and the markers in the standard patterns, analyzing the coordinates to identify the standard patterns and; loading and aligning (B) the test wafer in both the average predicted coordinates and the actual coordinates for each of the located patterns, and then averaging over the multiple sets of actual coordinates; then using a non-linear least-squares program to calculate a set of alignment transformation parameters that converts the average predicted coordinates as nearly as possible to the actual coordinates.