Apparatus for nanofabrication on an unconventional substrate including a patterned pliable membrane mechanically coupled to a membrane support structure, a substrate support structure to receive a substrate for processing, and an actuator to adjust the distance between the pliable membrane and the substrate. Nanofabrication on conventional and unconventional substrates can be achieved by transferring a pre-formed patterned pliable membrane onto the substrate using a transfer probe or non-stick sheet, followed by irradiating the substrate through the patterned pliable membrane so as to transfer the pattern on the pliable membrane into or out of the substrate. The apparatus and methods allow fabrication of diamond photonic crystals, fiber-integrated photonic devices and Nitrogen Vacancy (NV) centers in diamonds.