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Increased flexibility of patterning methods is important for the engineering of multimaterial and multifunctional nano/micro-electro-mechanical systems (NEMS/MEMS), such as polymer-based electronic and sensor devices, 3D microfluidic systems, and bio-analytical systems. Stencil lithography is a good candidate as it is a resistless, single step patterning method based on direct, local deposition of material on an arbitrary surface through a solid-state membrane, e.g. a 200-nm thick silicon nitride (SiN) membrane. We present two new stencil membrane stabilisation geometries and associated MEMS processes that allow for advancing further towards a well-controlled full-wafer (100 mm) nanostencil process for reproducible, high-throughput, large-area nanopatterning of mesoscopic structures (10-9 - 10-3 m). In fact, the major challenges for well-controlled and reproducible nanostencil lithography are to control stress-induced membrane deformation, clogging of membrane apertures and the gap between stencil and substrate. The stabilized membranes show improved membrane stability (i.e. reduced out-of-plane deformation) up to 94%, resulting in an improved pattern definition of stencil-deposited structures. We have also systematically characterized the clogging of membrane apertures and the influence of the gap between stencil and substrate on the deposited structures as a function of aperture size and deposited material. A method is presented to recover nominal dimensions of stencil-deposited structures over a gap. To integrate nanomechanical structures with CMOS circuits, stencil lithography was used as a clean, CMOS-compatible method to define the mechanical structures on a CMOS circuit, using the stencildeposited metal patterns as a mask for silicon reactive ion etching (RIE). When the stencil and the CMOS wafer are put in contact, a gap exists between the layer to be structured and the stencil. We have been able to correct the blurring effect by developing a controlled dry Al etch process. The results obtained provide a clear remedy to overcome one of the major challenges in nanostencil-based surface patterning. Stencil lithography is also used in the development of novel nanotemplates of anodic porous alumina (APA). To obtain APA structures with high regularity, a method to pre-pattern the surface of the aluminum substrate before conventional anodization is a prerequisite. A pre-patterned arrangement of dots or holes on Al plates is obtained by evaporation, sputtering, electrodeposition, or chemical etching through stencils. It should result in a high regularity mono-domain APA with pore spacing comparable with the visible wavelength for large area photonic crystals for optical applications and luminescence devices.