Stencil lithography is an innovative method for patterning that has a great flexibility from many points of view. It is based on shadow mask evaporation using thin silicon nitride membranes that allow the patterning of sub-100 nm features up to 100 μm in a single deposition. The stencil lithography does not require the coating or development of an organic resist and in addition the stencils can potentially be reused. This technique allows the use of contact or close proximity evaporations. These capabilities make stencil lithography an extremely flexible and clean technique. It can be used to evaporate a wide range of materials like metals, oxides, self-assembled monolayers, organic thin films, magnetic materials and in principle anything that can be deposited on a surface from a vapor phase. Its flexibility also includes the substrates for deposition, like silicon wafers, CMOS circuits, organic materials, non-planar substrates or fragile surfaces (like cantilevers or MEMS). It can also be extremely important for evaporation of sensitive materials that are degraded by development, etching or lift-off processes. The purpose of this project is to use stencil lithography for the fabrication and characterization of nanometer structures for nanoelectronic devices. We aim to develop devices based on silicon, but also on organic or flexible platforms. Our first goal is the patterning of nanowire structures made of different materials, focusing initially on Al, Au and Si. These materials are extremely important in modern semiconductor industry and its miniaturization is important for future nanoelectronic devices. Our target substrates are conventional silicon wafers and flexible PDMS (poly-dimethyl-siloxane) films. We will present results on the patterning of Al nanowires using stencil lithography and Si nanowires obtained after pattern transfer. The devices have lengths from 1 to 2 μm with widths of ~100 nm. For this purpose we used stencils with thin silicon nitride membranes patterned with focused ion beam (FIB) milling. The fabrication of the wires is based on the evaporation of 20 nm Al on SiO2/Si wafers through stencils containing nanoslits. This results in ~100 nm width Al nanowires that are used as masks for pattern transfer into Si wafers and poly-Si films using dry etching techniques. These results show the capability of the stencil technique for the patterning of ~100 nm nanowires using replication method that is cheap and clean. It also opens the possibilities of new fabrication methods for nanoelectronics on silicon but also on non-conventional substrates like PDMS.