A novel nanofabrication technique which can produce highly controlled silicon-based nanostructures in wafer scale has been proposed using a simple amorphous silicon (α-Si) material as an etch mask. SiO2 nanostructures directly fabricated can serve as nanotemplates to transfer into the underlying substrates such as silicon, germanium, transistor gate, or other dielectric materials to form electrically functional nanostructures and devices. In this paper, two typical silicon-based nanostructures such as nanoline and nanofin have been successfully fabricated by this technique, demonstrating excellent etch performance. In addition, silicon nanostructures fabricated above can be further trimmed to less than 10 nm by combing with assisted post-treatment methods. The novel nanofabrication technique will be expected a new emerging technology with low process complexity and good compatibility with existing silicon integrated circuit and is an important step towards the easy fabrication of a wide variety of nanoelectronics, biosensors, and optoelectronic devices.