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In fabricating high areal density magnetic nanostructures for bit patterned magnetic recording media, conventional lithography methods are limited in scaling and often present other challenges, for instance, as etch-damage in case of subtractive schemes. In this paper, we present a novel two-phase growth scheme that enables the fabrication of nanostructures of one material embedded in a matrix of a different material by choosing a separation material that is immiscible with the material of the nanostructure and by designing a template whose material and morphology guides the separation of the two phases and their subsequent growth.