We investigated the sputtering rate and surface morphology of polymethylmethacrylate (PMMA) samples bombarded with Ar cluster ion beam with selected energy of 12.5 eV/atom. The incident cluster energy range was 10–60 keV/ion. The incident cluster ion was selected before irradiation by using the time-of-flight (TOF) method. Both the sputtering rates and the average surface roughness increased rapidly with increasing incident cluster size under bombardment with small cluster ion. Under bombardment with large cluster ion, the average surface roughness does not increase rapidly, although sputtering rates increased nonlinearly. It suggests that a cluster ion beam with large size would be effective for high speed etching without roughing the surface.