Self-assembly represents a large prospective class of nanoscale fabrication techniques for future electronics. Understanding the mechanisms underlying the processes of nanostructure formation is crucial for establishing the control over their dimensions, spatial distribution, and uniformity. In this work, nanostructuring of Si was studied by silicon heteroepitaxy on NiSi2 nucleated at the Ni/Si interface during low-temperature Si sputtering on a thin Ni prelayer. The formation of spatially separated Si wires is discussed in terms of nucleation phenomenon, strain relaxation in the lattice-matched systems, and Si deposition kinetics.