Abstract Irradiation effects of Ar and O 2 cluster ion beams were studied on Chemical Vapor Deposition (CVD) diamond films. When the acceleration energy of the O 2 cluster ion was 20 keV, the sputtering yield was 400 atoms/cluster which is 13 times higher than that of Ar cluster ions because of the enhancement by chemical reactions. The average roughness of the diamond surface decreased with Ar cluster ion beams. This smoothing is attributed to the physical sputtering effect. However, a thin graphite layer was formed on the surface by contamination of monomer ion in the cluster beam, which decreases the optical transmittance of the diamond films. In contrast, the surface roughness was not improved but no graphite layer was formed with O 2 cluster ions. By using both Ar and O 2 cluster ion beams, a very flat diamond surface without a graphite layer on the surface can be fabricated.