Amine-active N-hydroxysuccinimide-terminated alkyl thiol templates are generated using parallel dip-pen nanolithography (DPN) and are used to covalently couple protein A/G. The protein arrays generated (see figure) are used to capture antibodies through affinity binding, while preserving their biological recognition properties. The versatility of the parallel DPN method for making many similar structures in a relatively high-throughput manner (14 000 dots in 10 min) is described.