We report a combined top-down/bottom-up hierarchical approach to fabricate massively parallel arrays of aligned nanoscale domains by means of the self-assembly of asymmetric polystyrene-block-poly(ethylene-alt-propylene) diblock copolymers. Silicon nitride grating substrates of various depths and periodicities are used to template the alignment of the high-aspect-ratio cylindrical polymer domains. Alignment is nucleated by polystyrene preferentially wetting the trough sidewalls and is thermally extended throughout the polymer film by defect annihilation. Topics discussed include a detailed analysis of the capacity of this system to accommodate lithographic defects and observations of alignment beyond the confined channel volumes. This graphoepitaxial methodology can be exploited in hybrid hard/soft condensed matter systems for a variety of applications.