The present invention relates to determining the location of a defect source which results in a localized elevation on the surface topography of a substrate such as, for example, a silicon wafer. The wafer is placed on a chuck of a semiconductor process tool such as, for example, a photolithographic tool. The upper surface of the wafer is processed by the photolithographic tool to obtain topography measurements. The topography measurements are analyzed to detect the presence of the localized elevation on the upper surface of the wafer. Once the presence of the localized elevation is detected, calculations are performed using the topography measurements to determine whether the source of the localized elevation results from the chuck.