Abstract Ion beam lithography was studied as an alternative approach for micro/nano machining of polymeric substrates. Our preliminary study was carried out using poly(methyl methacrylate) (PMMA) as a model system. Spin cast PMMA films were submitted to masked Ca + ion implantation (85 keV, 1×10 14 ions/cm 2), and P + ion implantations (85 keV, 1×10 15 and 1×10 16 ions/cm 2 respectively). The patterns generated on the films were characterized by AFM as arrays of holes with nanoscale depth and microscale width. The effect of ion implantation on surface property was investigated by measuring surface hydrophobicity. The results showed that masked ion beam lithography can change not only the surface topography, but also the surface hydrophobicity.