The effects of SiO2 reactive ion etching (RIE) in CFJ40% H2 on the surface properties of the underlying Si substrate have been studied by x-ray photoemission and He ion scattering/channeling techniques. The two major modifications of the Si near-surface region are: (i) A disordered Si layer which contains -1-2 • 10 TM displaced Si atoms/cm 2, the degree of the disorder depending on the plasma exposure time of the Si substrate. (ii) The presence of a -30~ thick film containing carbon and fluorine. The glow discharge deposited C,F-film exhibits a complex carbon ls x-ray photoemission spectrum and displays at least five bonding states of carbon. They are (in the order of decreasing intensity) C-C and/or C-H, C-CFx, CF, CF3, and CF2 type bonding. A new method for Si substrate post-RIE cleaning is described. The method accomplishes the removal of most RIE related surface residues and the removal of Si lattice disorder in one processing step. The efficacy of the method has been verified by ion scattering and x-ray photoemission measurements.