Low energy metal ion implantation of poly(dimethylsiloxane) (PDMS) films simultaneously allows for the creation of complex and tuneable topographical features at the surface, while also enhancing the biocompatibility of the surface for biological applications. PDMS thick films were implanted with Mg, Ta, and Fe at constant dose. Cells cultured on all of the modified surfaces enjoyed an increase in viable cell count of over 440% when compared to the pristine surface, with the Fe implanted surface showing a 600% increase with a substantial increase in surface energy, which was reflected by the increased contact angle. This was achieved without any biochemical patterning requiring multiple processing steps, complex chemistries, or clean room facilities. The rapid prototyping and ease of creation makes this technique useful for the fabrication of selective and functionalised substrates and scaffolds for in depth bio-analytic studies, implants, and device components. The results of surface energy studies, cross-sectional transmission electron microscopy, and compositional analysis, as well as initial biocompatibility testing, are presented. © 2011 American Scientific Publishers.