We report an alternative technique which utilizes fast proton or helium ion irradiation prior to electrochemical etching for three-dimensional micro-fabrication in bulk p-type silicon. The ion-induced damage increases the resistivity of the irradiated regions and slows down porous silicon formation. A raised structure of the scanned area is left behind after removal of the tin-irradiated regions with potassium hydroxide. The thickness of the removed material depends on the irradiated dose at each region so that multiple level structures can be produced with a single irradiation step. By exposing the silicon to different ion energies, the implanted depth and hence structure height can be precisely varied. We demonstrate the versatility of this three-dimensional patterning process to create multilevel cross structure and. freestanding bridges in bulk silicon, as well as sub-micron pillars and high aspect-ratio nano-tips.