Abstract Cleaning substrate surfaces and checking the effectiveness of the cleaning method are two very important aspects of reliable surface analysis. The absence of a cleaning process leading to an yttria‐stabilized zirconia (YSZ) surface that is free of contaminants and of unchanged structure has inspired us to investigate a new surface cleaning method based on a combination of high vacuum annealing at 300°C and oxidation with atomic oxygen. The efficiency of the cleaning procedure is examined by studying the surface composition after each stage of the process with low‐energy ion scattering (LEIS or ISS) and x‐ray photoelectron spectroscopy (XPS). The cleaning method results in complete removal of contaminants adsorbed from the ambient atmosphere, such as water and hydrocarbons. No segregation or sputtering effects due to the cleaning procedure are observed. The process also is compared with more conventional methods such as thermal oxidation and plasma etching. Although this study focuses on cleaning polycrystalline YSZ, which is inherently difficult to clean, other oxides and several metals also are investigated. For all the oxides studied, the newly proposed cleaning strategy removes up to ∼90% more contamination than the commonly used method of thermal oxidation. In the case of metals, the surface carbon is replaced by oxygen, which can be removed much easier. Additional segregation of bulk carbon is avoided. Copyright © 2002 John Wiley & Sons, Ltd.