Using low-energy electron microscopy we show that Au deposition leads to the arrangement of three-dimensional islands at surface atomic steps on Si(111). Because the islands nucleate within a narrow coverage window, they have a small size distribution and their size can be precisely controlled by the deposition time. During the Au deposition on the surface with a controlled island density, the islands move into upper terraces with trenches left behind. This indicates that the islands are Au-Si alloy droplets. The Au-Si alloy islands act as catalysts for the nanowire formation based on the vapor-liquid-solid (VLS) mechanism, which enables us to fabricate the one-dimensional alignment of vertical GaP nanowires. Controlling the size and position of the nanostructures by using surface atomic steps as templates means “top-down” lithographic techniques are not needed. Our method is a pure “bottom-up” self-assembly one and is expected to greatly contribute to establishing self-assembled nano-device fabrication methods.