A system and method for processing large area substrates. In one embodiment, a system for processing large area substrates includes prep station, a stamping station and a stamp that is automatically moved between the stamping station and the prep station. The stamping station is adapted to retain a large area substrate thereon. The stamp has a patterned bottom surface that is adapted for microcontact printing. The prep station is for applying a precursor to the patterned bottom surface of the stamp. In one embodiment, a method for processing large area substrates includes the steps of disposing a large area substrate on a platen, inking a stamp adapted for microcontact printing, and automatically contacting a bottom of the stamp to the large area substrate supported on a platen.