The research and development by AMMTRA (Advanced Material-processing and Machining Technology Research Association) of ion beam systems and processing technology, and selected research projects funded in part by Grants-in-Aid on Priority Areas from the Ministry of Education are reviewed. The AMMTRA projects, including five advanced industrial-scale ion beam systems and two processing projects, for silica glass and metal surface modifications, are described. Major research projects which have been funded by the Ministry of Education include X-ray imaging optics, and metal semiconductor interfaces. Ionized cluster beam deposition has been applied in those projects to form highly reflective mirror surfaces and semiconductor metallization with epitaxial metal films.