This paper presents a complex experimental and theoretical study of the droplet epitaxial growth of In/GaAs(001) nanostructures on patterned surfaces. We observe that holes formed after GaAs overgrowth of surfaces treated with a focused ion beam are the preferred centers for the nucleation of In droplets at any temperature in a range from 250 °C to 350 °C. Good selectivity and localization of droplets are achieved along a square perimeter of holes located at a distance from 0.5 to 4.2 µm apart. However, lower temperatures are required to provide filling of more holes and formation of an ordered array of droplet pairs. Using kinetic Monte Carlo simulations, we demonstrate growth conditions which allow filling of all holes located at variable distances in a range from 20 to 340 nm and avoiding unnecessary nucleation beyond the holes.