This paper discusses the suppression of self-assembled silicon nanostructure growth through high fluence ion implantation. The nanofabrication procedure involves annealing of untreated Si(100) substrates at 1100 °C for 15 s using a raster scanned 20 keV electron beam. Nanostructuring occurs as a result of kinetic amplification of the surface disorder induced by thermal decomposition of the native oxide. Radiation induced disorder of the Si substrate prior to annealing by ion-implantation modifies the potential energy surface and thus the growth of self-assembled nanostructures. Highly disordered Si(100) surfaces produced by high fluence implantation with nitrogen and silicon ions are shown to completely suppress nanostructure growth. Exploiting this phenomenon we have demonstrated selective area nanostructure growth in microscale regions.