Silicon wafers with thermal silicon oxide layers were cleaned and hydrophilized by three different methods: (1) the remote chemical analysis (RCA) wet cleaning by use of ammonia and hydrogen peroxide mixture solutions, (2) water-vapor plasma cleaning, and (3) UV/ozone combined cleaning. All procedures were found to remove effectively organic contaminations on wafers and gave identical characteristics of the contact angle, the surface roughness and the normal force interactions, measured by atomic force microscopy (AFM). However, it is found that wafers cleaned by the RCA method have several times larger friction coefficients than those cleaned by the plasma and UV/ozone methods. The difference was explained by the atomic-scale topological difference induced during the RCA cleaning. This study reveals the lateral force microscopy as a very sensitive method to detect the microstructure of surfaces. (c) 2006 Elsevier Inc. All rights reserved.