We developed a polyatomic cluster ion beam system for materials processing, and polyatomic clusters of materials such as alcohol and water were produced by an adiabatic expansion phenomenon. In this article, cluster formation is discussed using thermodynamics and fluid dynamics. To investigate the interactions of polyatomic cluster ions with solid surfaces, various kinds of substrates such as Si(100), SiO2, mica, polymethyl methacrylate, and metals were irradiated by ethanol, methanol, and water cluster ion beams. To be specific, chemical reactions between radicals of polyatomic molecules and surface Si atoms were investigated, and low-irradiation damage as well as high-rate sputtering was carried out on the Si(100) surfaces. Furthermore, materials processing methods including high-rate sputtering, surface modification, and micropatterning were demonstrated with ethanol and water cluster ion beams.