A method and apparatus that accurately marks a wafer at selected locations such as a defect location on the surface of a wafer such that a wafer analysis system (e.g., SEM or AFM) may rapidly find the defect. The apparatus contains a wafer platen for retaining a wafer in a substantially horizontal orientation and a marking assembly mounted above the wafer platen. The marking assembly further contains an optical microscope and a marking head. In operation, a user locates a defect using the optical microscope and places a pattern of fiducial marks at a predetermined distance from the defect, e.g., four marks in a diamond pattern circumscribing the defect.