This study describes the preparation of biocompatible patterned surfaces by a two-photon absorption technique. We have synthesized poly(2-methoxyethyl acrylate) copolymers, which exhibit biocompatibility and photocrosslinking moiety. Fabrication resolution can be controlled in the sub-micrometer range by changing the laser power, photoinitiator concentration, and scanning speed. The patterned surfaces showed excellent human platelet compatibility. Biocompatible patterned surfaces can be used in various medical devices, implants, biosensor chips, and tissue engineering scaffolds.