The following five wet cleaning methods have been compared as substrate preparation for molecular beam epitaxy (MBE) (1) modified Shiraki, (2) H2SO4/H2O2 treatment, (3) H2SO4/H2O2/HF treatment, (4) RCA, and (5) RCA + HF dipping The induced surface microroughness was estimated by atomic force microscopy. Residual carbon and oxygen were evaluated by secondary ion mass spectroscopy after capping layer,growth by MBE using Si2H6. Microroughness induced by SPFM treatment is similar to that of others. H2SO4/H2O2/HF treatment showed superior ability of carbon and oxygen removal. The oxide formed by H2SO4/H2O2/HF treatment can be removed at lower substrate temperature.