The preparation of clean Si and SiO2 substrates for basic semiconductor processing has become a more important technical problem as device geometries are reduced in order to increase the active element densities of VLSI- and VHSIC-integrated circuits. The traditional surface analysis techniques such as Auger spectrometry and ESCA analysis no longer have sufficient sensitivity to detect and quantitate the surface impurity levels. Therefore, a program to apply secondary ion mass spectrometry (SIMS) analysis to the first several nanometers at the surface of wafers undergoing cleaning processing has been undertaken. After determining the SIMS instrumental parameters needed to perform reproducible analyses, wafers cleaned by FSI-A, aqua regia, fuming nitric acid and Piranha plus HF cleaning procedures were analyzed. Each cleaning procedure removed some of the alkali elements (Na, K) but the difference between the best and worst performance gave greater than a factor of 10 variation in surface alkali content. Typical wafer contaminants (Mg, Ca, Cr, Cu, Al, and B) were removed with greatly differing efficiency by the various cleaning processes used. Data on the relative efficiencies of the various cleaning processes and their suitability for different contaminants will be presented. In addition, an example of a contaminated thin-deposited nitride film analysis will be presented.