Here, we present a two-step annealing procedure to imprint nanofeatures on SiO2 starting from metallic microfeatures. The first annealing transforms the microfeatures into gold nanoparticles and the second imprints these nanoparticles into the SiO2 layer with nanometric control. The resulting nanohole arrays show a high ensemble uniformity. As a potential application, the nanohole mask is used as a selective mask for the Ga self-assisted growth of GaAs nanowires (NWs). Thus, for the first time, a successful implementation of nano-self-imprinting that links high-throughput microlithography with bottom-up NW growth is shown. The beneficial hole morphology of the SiO2 mask promotes high Ga droplet contact angles with the silicon substrate and the formation of single droplets in the mask holes. This droplet predeposition configuration enables a high vertical yield of NWs. Thus, this article describes a new protocol to grow NW devices that combines simultaneously nanosized holes and parallel processing.