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Nanosphere lithography (NSL) is a technique capable of creating large-area arrays of small objects with tailor-made shapes. Here we present an algorithm, which simulates the shape and morphology of nanoparticles produced via NSL in combination with physical vapor deposition from variable angles. The key idea is based on a ray-tracing technique. Mask clogging effects have a major influence on the shape of resulting nanoobjects and are therefore taken into account. In addition, we implemented a metaball concept for the precise description of thermally modified masks. The calculated results are compared exemplarily with atomic force microscopy (AFM) data of experimentally fabricated nanostructures.