This study demonstrates a novel technique for the fabrication of ordered arrays of Au rich nanoparticles on a Si substrate. Si substrates, with their native oxides intact, are pre-patterned using nanoindentation to create regions on the surface that readily alloy at higher temperatures with a thin thermally evaporated Au layer. Larger Au rich particles are observed to form at the indentation sites after high temperature annealing in an inert atmosphere. After mechanical wiping, the Au rich particles lying within the indentation sites remain while almost all the particles on the native oxide surface are readily removed. Using PECVD techniques, multi-prong Si nanowires are shown to grow from the remaining arrays of Au rich particles.