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 work addresses phenomena associated with stencil nanopatterning and presents the results of modelling and simulation studies for predicting the deleterious effects of mask deformation, geometry of deposition setup, clogging and their combined effect during pattern transfer. This simulation work relates stencil initial geometry and deposition parameters with the resulting geometry of patterned structures and allows assessment of pattern transfer resolution and process window definition.