Polyimide Kapton films with a thickness of 62 mu m were bombarded by Ar+, N+, He+ and D+ ions at energies from 10-50 keV. After bombardment at room temperature, the surface topographic changes of the polymer were investigated using an atomic force microscope (AFM). The most common feature of the ion-bombarded Kapton surface is the formation of craters which often have circular shape and rims. The crater sizes suggest they are unlikely to have been caused by a single ion but by the collective effects including diffusion and trapping of gas atoms and gas molecules in ion-bombarded polymer. A model for the formation of these craters is proposed.