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In situ reflection spectroscopy is demonstrated to be a useful technique for monitoring the damage to the surface of GaAs substrates induced by ions from an electron cyclotron plasma. Distinct differences in the reflectance spectra of GaAs substrates are observed between etching by argon ions and chemical cleaning by hydrogen ions. For argon it is found that the damage layer thickness increases linearly with the argon ion energy. Hydrogen ions induce a damage layer of 3.1 nm and arsenic atoms are preferentially removed from the surface as the ion energy increased.