Protein molecules on solid surfaces are essential to a number of applications, such as biosensors, biomaterials, and drug delivery. In most approaches for protein immobilization, inter-molecular distances on the solid surface are not controlled and this may lead to aggregation and crowding. Here, a simple approach to immobilize individual protein molecules in a well-ordered 2D array is shown, using nanopatterns obtained from a polystyrene-block-poly(2-hydroxyethyl methacrylate) (PS-b-PHEMA) diblock copolymer thin film. This water-stable and protein-resistant polymer film contains hexagonally ordered PS cylindrical domains in a PHEMA matrix. The PS domains are activated by incorporating alkyne-functionalized PS and immobilizing azide-tagged proteins specifically onto each PS domain using “Click” chemistry. The nanometer size of the PS domain dictates that each domain can accommodate no more than one protein molecule, as verified by atomic force microscopy imaging. Immunoassay shows that the amount of specifically bound antibody scales with the number density of individual protein molecules on the 2D nanoarrays.