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The development of nanodevices demands for patterning methods in the nanoscale. To bring nanodevices to the market, there is a need for fast, low-cost nanopatterning methods. In addition, an increased flexibility 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 surface micro/nanopatterning methods based on MEMS tools are currently being developed, e.g. 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, exposure and etch steps. MEMS tools combine a series of unique advantages: (i) compliant cantilevers can be made in silicon, dielectrics and also polymers , (ii) nm-sharp tips form a ‘mechanical zoom’ from micro to nanoscale, (iii) the mechanical frequency scales with size and mass and allows for resonances in the MHz range, (iv) low spring constants allow for application on fragile surfaces, (v) micromachining processes enable parallel, high density systems. MEMS-based nanopatterning can be implemented in various manners: as scanning devices for the flexible, serial, writing of nanopatternings, as replication tools for the copying of an existing pattern, or as parallel scanning MEMS systems combining both, flexibility and increased areal through-put. 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. Although the method faces several challenges in terms of membrane fabrication at 100-nm scale, gap control, mechanical stability, aperture clogging, alignment for multi-layer patterning, etc. the technique has tremendous advantages when applied to fragile substrates. 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, and 3D microfluidic systems).