Epitaxial growth requires an initial surface that is ordered and as free as possible of contaminants such as C, O, or metallic impurities. Wet chemical etching of Si(111) wafers by a solution of HF in alcohol after a modified RCA clean, has been shown to produce (1 × 1) H-terminated hydrophobic Si surfaces that are ordered at room temperature and can be desorbed at 200°C in UHV. Less is known about a similar treatment on Si(100) wafers, more commonly used in semiconductor technology. However, high temperature ( T > 800°C) thermal desorption of the native oxide on Si(100) is known to induce detrimental effects such as surface roughness, precipitation and dopant segregation. Therefore, this study is motivated by the development of a low-temperature ( T < 600°C) surface cleaning method for Si(100). RBS combined with ion channeling and nuclear reaction analysis is conducted to measure the coverage of C, O, and H as well as the residual disorder at the surface at different steps of wet chemical cleaning prior to low temperature desorption. Hydrogen is detected by the forward elastic recoil of H by 4He 2+ at 2.8 MeV. O and C are detected by nuclear reaction analysis (NRA) at 3.05 and 4.265 MeV, respectively, in combination with ion channeling along the Si〈111〉 direction to increase the detection sensitivity for C and O as well as to measure the Si surface peak to correlate it to surface disorder. Atomic force microscopy of these surfaces has shown different degrees of roughness in addition to defect formation and is correlated to the ion beam analysis results. Our results indicate a strong dependence of final H-passivation on the pretreatment of the Si surfaces before the final dip in the HF/alcohol solution.