The film thickness and surface damage layer of vapor-deposited L-leucine amino acid films irradiated with Ar cluster ion beams were characterized by PSC(R)A ellipsometry. The damaged layer on the surface of the L-leucine film irradiated with Ar cluster ion beam was quite thin, less than 1 nm in thickness. In contrast, films irradiated with Ar monomer ion beam have changed into totally different films. The ellipsometry method also allowed accurate measurements of the sputtering yield from the L-leucine film irradiated with Ar cluster ion beams at nm-order resolution. These results suggested that with proper analysis, the optical method of ellipsometry enables estimation of the surface damage layer and measurement of sputtering yield of organic films irradiated with cluster ion beams. Copyright (C) 2010 John Wiley & Sons, Ltd.