This work demonstrates, for the first time, the selective formation of ordered arrays of vertical GaAs nanowires on Si(111) with a native oxide layer using a two-step pre-treatment of the substrate surface with a focused Ga-ion beam. Based on our previous studies, we show that modifying the substrate through a two-step protocol — first applying a continuous surface treatment with low doses (up to 1×10–13 C/µm2), followed by spot treatment with medium doses (from 1×10–13 to 1×10–12 C/µm2) — effectively suppresses parasitic growth and enables nanowire formation at defined surface locations. Furthermore, adjusting the spacing between ion implantation points (from 0.5 to 5 um) allows precise control over the pitch of the nanowire array. By optimizing dose values, we achieve the formation of single, free-standing, vertically oriented nanowires at each ion beam impact site. The study of optical properties of nanowire arrays reveals their high structural quality, as evidenced by intense photoluminescence of GaAs up to room temperatures.