In this study, the fabrication of a wettability patterned surface for cellular micropatterning was investigated using step-wise ion beam processing. A perfluorinated poly(ethylene-co-propylene) (FEP) film was first irradiated using accelerated Xe+ ions with 100 keV of energy at the low current density of 1 μA/cm² over the entire surface. Second, its confined regions were irradiated at the higher current density of 15 μA/cm² at various ion fluences through the pattern mask to generate patterns with big differences in wettability. From the analytic results, it was clearly verified that the step-wise irradiation induced effective chemical and morphological changes on the FEP surface, resulting in the successful formation of well-defined micropatterns with relatively hydrophilic and superhydrophobic surfaces. Moreover, the results of in-vitro cell culture showed well-resolved formation of 200 μm cell micropatterns on the wettability patterned FEP surface due to the individual effects of the relatively hydrophilic and superhydrophobic properties on the cell adhesiveness and proliferation.