Template-guided self-assembly is one of the most promising approaches for creating functional nanosystems and effective methods are needed in order to generate micro and nanoscale templates for a diverse type of materials necessary for different applications. In this paper a plasma lithography technique is demonstrated which can directly pattern a wide variety of substrates including polystyrene, PDMS and glass for self-assembly of nanomaterials. The technique employs a deformable mold made using PDMS replication molding. The mold protects selective areas of the substrate from plasma surface treatment, which will spatially alter the surface properties of the substrate. Nanomaterials will then selectively self-assemble onto the pattern. Three-dimensional control is achieved by means of mold geometry and self-assembly conditions. Nanomaterials including nanoparticles, proteins, and salts have been patterned on configurations from arrays of lines and dots to arbitrary shapes in sizes ranging from millimeters to hundreds of nanometers.