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One of the ultimate tasks for stencil lithography is the ability to fabricate arrays of structures with controlled dimensions on the nanometer scale precisely positioned on a suitable surface. The race to shrink feature sizes requires the limits of conventional lithography to be extended to high-throughput, low cost, reliable and well-controlled processes of which stencilling is a promising candidate for nanoscale applications. Identifying, predicting and overcoming issues accompanying nanostencil lithography is critical to the successful and timely development of this technique for a wide range of potential applications. This paper addresses phenomena associated with stencil nanopatterning and presents the results of modelling and simulation studies for predicting the deleterious effects of mask distortion and clogging during pattern transfer. It is shown that degrading effects of stress-induced deformation of stencils can be dealt with via optimal design of corrugation structures which in turn reduce stencil deformation and significantly improves pattern definition. Modelling results are validated by comparison to experiment. The corrugation structures can be used to define practical design rules for fabrication of stable large area (‘‘full scale’’) purpose-designed stencil membranes. The accurate modelling of the clogging phenomenon combined with gradually evolving stencil deformation, also presented in the paper, can be used for prediction of pattern distortion, to calculate maximum thickness of a deposited layer and/or for prediction of the stencil lifetime.