Methods and systems for determining a position of a defect in an electron beam image of a wafer are provided. One method includes determining a second position of a defect with respect to patterns imaged in a test image based on a first position of the defect in a difference image. The method also includes determining a third position of the defect with respect to the patterns in an electron beam image for the defect and determining an association between the first and third positions. In addition, the method includes determining a position of another defect in an electron beam image based on a first position of the other defect in a difference image and the determined association.