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Sub-micron lithography processes are continuously optimized for semiconductor products where the enormous market potential justifies investment in advanced methods and extremely sophisticated equipment. Due to the extreme process costs and due to the limited process versatility in terms of substrates, processing and materials, these high-end methods can not be applied for the engineering of multi-material and multifunctional nano/micro-electro-mechanical systems (NEMS/MEMS), such as polymer-based electronic and sensor devices, 3D microfluidics, and bio-analytical systems. Often standard lithography methods can not be applied because the surfaces to be structured are either mechanically unstable, such as for cantilevers and membranes, and/or chemically functionalised for bio-sensor applications. To overcome the cost and process issues, a series of alternative surface patterning methods are currently being developed. The do not rely on photoresist technology and thin-film etching, and they are potentially low-cost. Well-known methods are e.g. scanning probe lithography, DipPen or NADIS lithography, or replication using soft-lithography and nanoimprint lithography. Another emerging method is based on the direct local deposition of thin film patterns through the apertures in miniature shadow-masks or nanostencils. E-beam or focused ion beam prepared stencils demonstrated sub-100 nm scale shadow nanofabrication on a small surface area. Recently we have made further progress in scaling up the nanostencil method to full-wafer scale, and by using it for various deposition methods on various sample surfaces. The presentation will first give an overview of the state-of-the-art of emerging nanopatterning methods that are based on micro-mechanical (MEMS) tools such as scanning probes and thin membranes. In particular, details on a combined DUV-MEMS process will be presented on the fabrication and application of nanostencils on a 100-mm size full-wafer.