Smoothing effect is one of the advantages of cluster ion beam. It is important to estimate an ion dose to achieve required surface smoothness. The smoothing rate with cluster ion beam depends on surface profiles. In this work, modeling of surface smoothing process with cluster ion beams was examined. Ar cluster ions with an energy of 20 keV was irradiated on rough Si Surface. Fast Fourier transform was applied to atomic force microscope data of 100 × 100 μm 2, and power spectra were calculated. Smoothing rate depends on the wave number as well as the ion dose. Relationship between smoothing rate and wave number was derived. The surface smoothing process was modeled with the use of the wave number dependence of the smoothing rate. The calculated and the experimental surface profiles are in good agreements.