Alkylsiloxane self-assembled monolayers ( SAMs) are used in the semiconductor industry and, more recently, as proxies for organics adsorbed on airborne mineral dust and on buildings and construction materials. A number of methods have been used for removing the SAM from the substrate after reaction or use, particularly plasmas or piranha ( H2SO4/H2O2) solution. However, when the substrates are reused to make new SAMs, the impact of the cleaning methods on the chemistry of subsequently formed SAMs on the surface is not known. Here we report atomic force microscopy, X-ray photoelectron spectroscopy, Auger electron spectroscopy, and Fourier transform infrared studies of changes in a silicon substrate upon repetitive deposition and removal of SAMs by these two methods. It is shown that a thicker layer of silicon oxide is formed, and the surface becomes irregular and roughened, particularly after the piranha treatment. This layer of silica impacts the structure of the SAMs attached to it and can serve as a reservoir for trace gases that adsorb on it, potentially contributing to the subsequent reactions of the SAM. The implications for the use of such surfaces as a proxy for reactions of organics on airborne dust particles and on structures in the boundary layer are discussed.