In order to investigate the interactions of methanol cluster ion beams with solid surfaces, Si substrates and SiO2 films were irradiated at different acceleration voltages. The sputtered depth increased with increase of the acceleration voltage. When the acceleration voltage was 9 kV, the sputtered depths of Si and SiO2 at a dose of 1×1016 ions/cm2 were 1497.1 nm and 147.8 nm, respectively. The selectivity between Si and SiO2 surfaces arose from the volatility of the reaction products. Furthermore, the sputtering yield for the Si surface was approximately seven hundreds times larger than that by Ar monomer ion beams. This suggested that chemical sputtering was predominant for the methanol cluster ion irradiation. In addition, the etching and cleaning process by the methanol cluster ion irradiation was performed on the Si surfaces contaminated with a small amount of metal particles such as Au and Al. Thus, methanol cluster ion beams have unique characteristics such as surface etching and cleaning with high sputtering yield and smooth surface.