We reveal a novel phenomenon observed after self-catalytic growth of GaAs nanowires on Si(111) substrates treated with a Ga focused ion beam (FIB). Depending on the ion dose, nanowire arrays with various geometrical parameters can be obtained. A minor treatment of the substrate enables a slight increase in the surface density of nanowires relative to an unmodified substrate area. As the ion dose is increased up to ~0.1 pC/µm2, the growth of GaAs nanowires and nanocrystals is suppressed. However, a further increase in the ion dose stimulates the crystal growth leading to the formation of extremely thin nanowires (39 ± 5 nm) with a remarkably high surface density of up to 15 µm-2. Resting upon an analysis of the surface structure before and after stages of ion-beam treatment, ultra-high vacuum annealing and nanowire growth, we propose a mechanism underlying the phenomenon observed. We assume that the chemical interaction between embedded Ga ions and a native Si oxide layer leads either to the enhancement of the passivation properties of the oxide layer within FIB-modified areas (at low and middle ion doses), or to the etching of the passivating oxide layer by excess Ga atoms, resulting in the formation of pores (at high ion doses). Due to this behavior, local fabrication of GaAs nanowire arrays with a diverse range of characteristics can be implemented on the same substrate. This approach opens a new way for self-catalytic growth of GaAs nanowires.