Nanofabrication on insulating and flexible films of polydimethylsiloxane (PDMS) using a focused ion beam (FIB) has been illustrated in this study. The charge accumulation effect, which is inevitable in polymeric fabrication, was shown to be relieved by simultaneously introducing electron beam flooding in the area exposed to FIB. The topography of the fabricated pattern is subsequently characterized by using an atomic force microscope (AFM), by which the dependence of height/depth of the fabricated arrays on ion beam dose could be obtained. In addition, the swelling effect and milling effect relating to focused ion beam dose could be identified in this study.