A protocol for electrochemical cleaning of carbon-contaminated alkanethiol SAMs at mechanically polished (MP) Ag surfaces is characterized by surface Raman spectroscopy and electrochemistry. Vibrational information in the nu(C-S), nu(C-C), nu(C-H), and delta(C-H) regions is particularly useful in elucidating the degree of order and amount of contamination in propanethiol, dodecanethiol, and octadecanethiol monolayers before and after negative potential exposure in several aqueous electrolytes. Specifically, Raman spectra indicate that electrochemical cleaning of alkanethiol SAMs at potentials negative of the thiolate reduction removes carbonaceous species and greatly increases the film order near the sulfur headgroup.