Nanopatterned ZnO nanowire arrays are fabricated in large scale on epitaxial GaN substrates through a template-controlled process. This process involves nanosphere self-assembly and mask transfer, deposition of Au nanodots, and vapor-liquid-solid (VLS) growth of ZnO nanowires. Self-assembled polystyrene nanospheres are transferred from hydrophilic glass substrate onto hydrophobic GaN layers using an elegantly simple mask transfer technique. Gold is thermally evaporated through the nanosphere mask to form ordered arrays of Au nanodots. Subsequently, ZnO nanowires are grown via VLS epitaxy mechanism catalyzed by the Au nanodots. The diameters and lengths of the nanowires are strongly correlated with the Au dot sizes and growth time, respectively. Cross-sectional transmission electron microscopy studies confirm the VLS epitaxy mechanism and the single crystallinity of the nanowires. PACS: 61.82.Rx; 81.05. Keywords: A1. Nanosphere lithography; A1. Nanostructures; A3. Vapor-phase epitaxy; B1. nanomaterials; B1. Zinc compounds; B2. Semiconducting II-IV materials