In this work, we characterized the surface damage layer and sputtering yield of polycrystalline L-leucine films before and after irradiation with Ar cluster or monomer ion beams with x ray photoelectron spectroscopy and ellipsometry. Irradiation with Ar monomer ion beams induced heavy damage on the surface of L-leucine films, such as bond breaking and carbonization. In contrast, no significant surface damage was observed in the films irradiated with Ar cluster ion beams. The sputtering yield of L-leucine decreased dramatically with increasing fluence of monomer Ar ions and approached the value of the sputtering yield of graphite; but under irradiation with Ar cluster ion beams, the sputtering yield remained constant with fluence. The differences in sputtering yield behavior were explained in relation with the surface damage layer on organic materials. Thus, cluster ion beams could potentially be used to mill down biological materials without significant damage on the surface and could contribute to various applications in the analysis and processing of life matter. (C) 2011 American Institute of Physics. [doi:10.1063/1.3658220]