A matrix of Si crystals can be formed on amorphous substrates by manipulating nucleation sites. We have investigated various SiNxby x‐ray photon spectroscopy in order to search for suitable artificial nucleation sites and measured the density of Si nuclei deposited on the SiNx. It is found that the Si/N compositional ratio of the Si+ion implanted SiNxsurface is much higher than the theoretically estimated value. Si nucleus density on these surfaces increases with the Si/N compositional ratio. Si crystals were well manipulated on the portions of the Si‐enriched SiNxdotted over SiO2due to improved selectivity.