The success of scanning probe microscopy in the imaging of biomolecules has led to the need for specially tailored image processing and data analysis routines. To permit the correlation of topographs with x-ray crystallographic and electron microscopy data, automated feature discrimination and measurement algorithms have been developed. Incorporation of statistical techniques, such as cluster analysis, have allowed surface features to be characterized into single molecules and aggregates where the number of molecules forming the clusters can be calculated. The application of these routines to topographic data of proteins collected in our laboratory has permitted accurate comparisons with information from complementary biophysical techniques to be made. We believe that such developments are critical for the continued success of probe techniques in the imaging of biomolecules.