Despite extensive research and much progress, it remains critical and challenging to precisely grow nanowires structurally and dimensionally uniform. Here, we present a focused-ion-beam (FIB) assisted approach to controlling the ZnO nanowire growth with uniform diameters, height, and high crystalline quality. Vertical-alignment is also achieved on nonepitaxial substrates without the assistance of ZnO seeding layers (e.g., silicon and c-plane sapphire substrates). The programmable ability of FIB opens up new opportunities of creating complex patterns in our approach. A new alloy catalyst Au-Ga is developed for ZnO growth, with achievable narrow nanowire size distributions. Comparison studies of growth behavior in the temperature range 880-940 degrees C for Au and Au-Ga catalysts reveal different growth kinetics and rate-controlling mechanisms that are consistent with the vertical-alignment and drastically improved nanowire uniformity for FIB-assisted nanowire growth. Nanogenerators built with the improved nanowire platform exhibit a 2.5-fold increase in thermal energy conversion, demonstrating the promise of our approach for advanced functional devices.