Local wafer thickness variation is a significant source of defocus error for submicron lithography. A method of characterizing the flatness of wafers using the auto-focus system of a stepper is developed. An analysis of the data is carried out by a program that provides the distributions of TTV (total thickness variation), LTV (local thickness variation) and LAV (local averaged thickness variation). Contour mapping of the average height per field across a wafer can reveal the areas where the most or least rapid thickness changes are occurring, which can be caused by vacuum bending, chuck tilt, or the different polishing techniques used by vendors. The areas of investigation include a comparison of samples supplied by several silicon vendors, the effects of edge exclusion, and the impact of typical MOS process steps. Wafer flatness is correlated to critical dimension control. In the worst case, local thickness variation within a typical stepper field of more than four microns is observed on new, silicon wafers which causes resist bridging over a large portion of an image field. Finally, the potential benefit of wafer leveling systems is discussed.