We compare measurements of the roughness of silicon(001) wafers cleaned by several methods. The roughness values were obtained using crystal truncation rod (CTR) scattering and atomic force microscopy. Although they do not yield identical results, both methods show the same relative roughness for the different cleans. CTR scattering is sensitive to roughness on lateral length scales down to atomic dimensions. The quantitative differences in roughness can be explained by the different wavelength spectrum of roughness probed by the two techniques. CTR measurements were also performed after a 60 Å thermal oxide was grown on the wafers. The roughness trends are the same after oxidation, but we also find that the oxidation process has significantly reduced the interfacial roughness. ©1997 American Institute of Physics.