Methods and systems for detecting defects on a wafer are provided. One method includes identifying one or more characteristics of first raw output generated for a wafer that correspond to one or more geometrical characteristics of patterned features formed on the wafer and assigning individual output in second raw output generated for the wafer to different segments based on the identified one or more characteristics of the first raw output and based on the individual output in the second raw output and individual output in the first raw output that were generated at substantially the same locations on the wafer such that the one or more geometrical characteristics of the patterned features that correspond to each of the different segments in the second raw output are different.