The interaction of H(D) atoms with alkylsiloxane self-assembled monolayers deposited on oxidized Si(100) has been examined under ultrahigh vacuum conditions. Using high-resolution electron energy loss spectroscopy, evidence is observed for the H/D exchange reaction. The reaction is initiated by hydrogen abstraction via an Eley-Rideal type mechanism to form an alkyl radical. For low exposures to H(D) atoms, the exchange reaction occurs relatively rapidly, as indicated by the rate of increase in intensity of the C-D stretch. As exposure increases, the exchange reaction slows due to steric effects. Etching of the monolayers also occurs, as indicated by the decrease in intensity of C-H modes and the increase in intensity of the Si-O modes of the underlying substrate upon exposure to atomic hydrogen. The presence of cross-linking is suggested by the rapid decrease in water contact angle as a function of H(D) exposure.