The endeavour to develop nanodevices demands for patterning methods in the nanoscale. To bring nanodevices to the market, there is a need for fast, low-cost replication nanopatterning methods. In addition, an increased flexibility of the nanopatterning 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. A series of alternative, complementary surface micro/nanopatterning methods are currently being developed, e.g. local printing of molecular layers (soft-lithography), local fluidic dispensing (NADIS), and shadow-mask deposition (nanostencil lithography). These methods rely on locally adding material onto the substrate without the need for resist layers and etching steps. Nanostencil lithography 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 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. To limit pattern deformation and blurring, i.e. reduced sharpness of edges and limited spatial detail, we have developed two schemes to incorporate in-situ, local stabilization structures in the stencil membranes. These stabilization structures are adaptable to the membrane apertures and they do not interfere with the material flux during deposition. 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 and will present the clogging of membrane apertures as a function of their size and deposited material. Cu and Ti thin-film deposition through 500-nm thick SiN stencil membranes resulted in half of the film thickness (that was evaporated onto the membrane surface) deposited at the inner sides of the membrane apertures. The stabilized membranes are easier to clean with a reduced risk of damage, increasing the reusability of the stencils. Furthermore, the influence of the gap between stencil and substrate on the deposited structures was determined quantitatively. We have studied patterning by stencil lithography of metals (Al, Au, Bi, Cr, Ti, Cu) on various surfaces (Si, SiO2, SU-8, PDMS, PMMA, freestanding SiN cantilevers, curved surfaces, CMOS chips, and self-assembled monolayers (SAM)) for different applications (nanomechanical devices, (molecular) electronic devices, nanoscale Hall-sensor devices, 3D microfluidic systems).