In this paper, we present a study of the effect of the silicon substrate modification by focused ion beams on subsequent growth of GaAs layers by molecular beam epitaxy. We demonstrate that when samples exposed to the ion irradiation at various accelerating voltages and ion beam passes are annealed in the absence of the arsenic flux, an increase in the depth of the modified Si substrate areas occurs. At the same time, crystallization of gallium accumulations during annealing in the arsenic flux leads to the filling of holes formed during the ion bombardment. We reveal that the growth of GaAs on substrates with areas modified at an accelerating voltage of 30 kV and subjected to subsequent annealing in the arsenic flux at a temperature of 600oC is accompanied by the formation of nanowires, the density of which increases within areas with a large number of ion beam passes. The results of the conducted research can be used for the development of technological approaches to the formation of GaAs epitaxial layers on Si substrates. Keywords: molecular beam epitaxy, monolithic integration, gallium arsenide, silicon, focused ion beams.