Examples are presented that application of amorphous Al x O y nucleation layer is an efficient way of controlling spatial distribution of GaN nanowires grown by plasma-assisted molecular beam epitaxy. On GaN/sapphire substrates Al x O y stripes induce formation of GaN nanowires while a compact GaN layer is formed outside the stripes. We show that the ratio of nanowire length h to the thickness of the compact layer d can be tailored by adjusting impinging gallium and nitrogen fluxes. Calculations of the h/d aspect ratio were performed taking into account dependence of nanowire incubation time on the growth parameters. In agreement with calculations we found that the value of h/d ratio can be increased by increasing the N/Ga flux ratio in the way that the N-limited growth regime determines nanowire axial growth rate while growth of compact layer remains Ga-limited. This ensures the highest value of the h/d aspect ratio. Local modification of GaN growth kinetics caused by surface diffusion of Ga adatoms through the boundary separating the Al x O y stripe and the GaN/sapphire substrate is discussed. We show that during the nanowire incubation period gallium is transported out of the Al x O y stripe, which delays nanowire nucleation onset and leads to reduced length of GaN nanowires in the vicinity of the stripe edge. Simultaneously the growth on the GaN/sapphire substrate is locally enhanced, so the planar GaN layers adopts a typical edge shape of mesa structures grown by selective area growth. Ga diffusion length on a-Al x O y surface of ∼500 nm is inferred from our results.