Photoresist-based lithography has major limitations when applied to micro-electro-mechanical systems (MEMS) with mechanically fragile and/or chemically functionalised surfaces. As a remedy, alternative, complementary nanopatterning methods have been developed, e.g. thermo-mechanical indentation (nanoimprint lithography), local printing of molecular layers (soft lithography), and shadow-mask deposition (nanostencil patterning). The nanostencil method is a resistless patterning method based on direct, local deposition of material on an arbitrary surface through a solid-state silicon nitride (SiN) membrane. In addition, the method offers the possibility of simultaneous deposition of micrometer and nanometer scale structures. Patterning of such mesoscopic structures (10^9 - 10^5 m) through stencils fabricated by MEMS processes in combination with focused ion beam (FIB) milling has been demonstrated within a limited area. In order to produce larger membranes enabling increased throughput of the nanostencil method, we developed a 100-mm wafer-scale (deep-UV) DUV/MEMS fabrication process. The mesoscopic patterns were first defined by a 4× reduced projection exposure using an ASML wafer stepper and then transferred into a SiN layer by means of reactive ion etching (RIE). The membranes were released by wafer-through etching using potassium hydroxide (KOH). Patterning of nano-scale structures using stencils allows for a large choice of materials and surfaces to be nanopatterned since no etch steps need to be applied. We have studied the nanopatterning of metals (Al, Au, Bi, and Cr) on various surfaces (silicon, oxides, freestanding SiN cantilevers, and self-assembled monolayers (SAM)) for different mesoscopic experiments. We will present details on the DUV/MEMS process and the application of the full-wafer stencil for specific applications such as templates for molecular electronics, nano-mechanical devices with a 90 MHz resonance frequency, as well as nano-scale Hall-sensor devices.