The reduction of substrate temperature is important in view of the integration of III–V materials with a Si platform. Here, we show the way to significantly decrease substrate temperature by introducing a procedure to create nanoscale holes in the native-SiOx layer on Si(111) substrate via In-induced drilling. Using the fabricated template, we successfully grew self-catalyzed GaAs nanowires by molecular-beam epitaxy. Energy-dispersive X-ray analysis reveals no indium atoms inside the nanowires. This unambiguously manifests that the procedure proposed can be used for the growth of ultra-pure GaAs nanowires.