We report a combined top-down/bottom-up hierarchical approach to fabricate massively parallel arraysof 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 periodicitiesare used to template the alignment of the high-aspect-ratio cylindrical polymer domains. Alignment isnucleated by polystyrene preferentially wetting the trough sidewalls and is thermally extended throughoutthe polymer film by defect annihilation. Topics discussed include a detailed analysis of the capacity of thissystem to accommodate lithographic defects and observations of alignment beyond the confined channelvolumes. This graphoepitaxial methodology can be exploited in hybrid hard/soft condensed matter systemsfor a variety of applications.