The mean value of a measurement set with precision a has an offset relative to an accepted standard. Calibration of an instrument involves subtracting the offset between the mean value and the reference. Unfortunately, imaging characteristics for most types of microscopes are not constant. Slight changes in feature wall angle, edge and surface roughness, or material properties can dramatically affect the precision and accuracy offset of the metrology instrument. Of course it would be impossible to fabricate a reference standard for every type of sample, as this would require an a priori knowledge of the feature characteristics as well as an infinite number of reference artifacts. Typically the process engineer will use in-house or "golden standards" to track the repeatability of a measurement tool. Unfortunately, variations in the features to be measured will cause the accuracy offset to change in ways that are unknown to the engineer. Furthermore, the offsets of multiple tools in a set will not only change with respect to the reference but also relatively to each other. It is the minimization of this relative offset between the various measurement tools that is referred to as matching. It should be noted that one could use a member in the nonreference set of tools, but then the question naturally arises of which one is most correct. It is desirable for a reference tool to provide the complete topography of a structure, as well as the ability to reduce the effects of sample variation (i.e., edge roughness) through spatial averaging. In this article, a method for using atomic force microscopes to provide reference values for matching of on-line scanning electron microscopes will be described.