We obtained HEED patterns for water cluster beams, which showed the cubic structure that is characteristic of ice. The intensity of the (111), (220), and (311) diffraction peaks increased with an increase in the vapor pressure. As an extension of the water cluster studies, a methane hydrate cluster was generated by a gas bubbling method. In addition, the fundamental phenomenon of water cluster ion irradiation was studied using photoluminescence measurements. The cluster ion beam-induced luminescence was observed, and the luminescence intensity increased with an increase in the acceleration voltage. This indicated that the kinetic energy was converted to thermal energy and the cluster temperatures as well as impact area could be very high. Furthermore, polymer substrates such as poly(methyl methacrylate) (PMMA), polyethylene terephthalate (PET), and polycarbonate (PC) were also subjected to irradiation by the water cluster ion beams, and the sputtered depth increased with an increase in the acceleration voltage. In particular, the sputtering yield of the PMMA surface was 206 molecules per ion at an acceleration voltage of 9 kV. Compared to the PET and PC surfaces, extremely high sputtering yield was obtained owing to the chemical modification of the PMMA surface by water cluster ion irradiation. [DOI: 10.1380/ejssnt.2016.144]