Developing fabrication methods for electronically active nanostructures is an important challenge of modern science and technology. Fabrication efforts for crystalline materials have been focused on state-of-the-art epitaxial growth techniques. These techniques are based on deposition of precisely controlled combinations of various materials on a heated substrate. We report a method that does not require deposition and transforms a nanoscale layer of a complex crystalline compound into a new material using low-energy ion-beam preferential etching (IBPE). We demonstrate this method by transforming a widely used insulator model system, SrTiO3, into a transparent conductor. Most significantly, the resistivity decreases with decreasing temperature as approximately T2.5+/-0.3 and eventually falls below that of room-temperature copper. These transport measurements imply a crystal quality in the conduction channel comparable to that obtained with the highest-quality growth techniques. The universality of low-energy IBPE implies wide potential applicability to fabrication of other nanolayers.