Polytetrafluoroethylene (PTFE) and fluorinated ethylene propylene (FEP) are well known as Teflon®. Synchrotron radiation and focused ion beam irradiation are effective techniques for fabricating microstructures on the surfaces of Teflon. In this study, we created micro-patterns between micro-protrusions on FEP surfaces by using a combination of 3 MeV proton beam writing (PBW) and subsequent 250 keV nitrogen ion beam irradiation. First, we found that the proton microbeam made bubbles inside FEP samples. After their samples were irradiated with the nitrogen ion beam, dense micro-protrusions were formed on the surfaces other than the upper parts above the bubbles. Instead, the parts became smooth or depressed along the patterns of PBW. Thus, a microfabrication of Teflon was demonstrated by using two different ion beam irradiation.