In this work, we present an attractive and novel fabrication technique that can produce highly-controlled silicon-based nanostructures in wafer-scale by a seldom used material in IC fabrication, amorphous silicon (α-Si), as an etch mask. The α-Si mask pattern is precisely transferred into the underlying SiO2 substrate material with a high fidelity by a novel top-down fabrication. It is the first time for α-Si film used as an etch mask to fabricate various Si-based nanostructures. It is observed that the α-Si mask can significantly reduce the pattern edge roughness and achieve highly uniform and smooth sidewalls. SiO2 nanostructures directly fabricated can be served 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. Several typical Si-based nanostructures, such as nanoline, nanofin and transistor gate patterning, have been fabricated successfully using the simple α-Si material combining with electron beam lithography. Our results demonstrate that the Si-based nanostructures as small as sub-20 nm may be achievable. More significantly, the novel approach is a potentially universal method that is fully compatible with the current existing Si-based CMOS technologies.