We describe a new approach for biomaterial patterning, viz, masked ion beam lithography. Poly (methyl methacrylate) (PMMA) film was used as a model system and subjected to Ca+ and P+ ion implantations through masks. Ca+ ion implantation was performed at an energy of 85 keV with a fluence of 1×1014 ions/cm2. P+ ion implantation was done at an energy of 85 keV with fluences of 1×1015 and 1×1016 ions/cm2. Arrays of holes were generated during these processes. AFM showed that the depth of the holes is in the nanoscale region. The surface hydrophobicity of the exposed PMMA films was investigated by contact angle measurement. The results indicated that ion implantation changed the surface hydrophobicity.