Atomic force microscopes (AFMs), which generate three dimensional images with nanometer level resolution, are increasingly being used as tools for sub-micrometer dimensional metrology in a wide range of applications. Measurements commonly performed with AFMs are feature spacing (pitch), feature height (or depth), feature width (critical dimension), and surface roughness. To perform accurate measurements, the scales of an AFM must be calibrated regularly. Presently available standards for this purpose are calibrated using stylus instruments and optical techniques. The effectiveness of this approach, however, is limited by the differences in the working ranges of the various techniques and by questions of methods divergence. Such divergence may occur between measurements made by instruments using different techniques to measure the same feature. A reflected light microscope and an AFM, for example, may have differing sensitivity to the cross-sectional profile of measured lines. For sufficiently steep lines, an AFM tip will only contact the features near the tops.