Hydrothermally synthesized zinc oxide nanowire arrays have been used as nanostructured acceptors in emerging photovoltaic (PV) devices. The nanoscale dimensions of such arrays allow for enhanced charge extraction from PV active layers, but the device performance critically depends on the nanowire array pitch and alignment. In this study, we templated hydrothermally-grown ZnO nanowire arrays via high-resolution electron-beam-lithography defined masks, achieving the dual requirements of high-resolution patterning at a pitch of several hundred nanometers, while maintaining hole sizes small enough to control nanowire array morphology. We investigated several process conditions, including the effect of annealing sputtered and spincoated ZnO seed layers on nanowire growth, to optimize array property metrics -branching from individual template holes and off-normal alignment. We found that decreasing template hole size decreased branching prevalence but also reduced alignment. Annealing seed layers typically improved alignment, and sputtered seed layers yielded nanowire arrays superior to spincoated seed layers. We show that these effects arose from variation in the size of the template holes relative to the ZnO grain size in the seed layer.The quantitative control of branching and alignment of the nanowire array that is achieved in this study will open new paths toward engineering more efficient electrodes to increase photocurrent in nanostructured PVs. This control is also applicable to inorganic nanowire growth in general, nanomechanical generators, nanowire transistors, and surface-energy engineering.2