Owing to its simplicity and low temperature conditions, magnesiothermic reduction of silica is one of the most powerful methods for producing silicon nanostructures. However, incomplete reduction takes place in this process leaving unconverted silica under the silicon layer. This phenomenon limits the use of this method for the rational design of silicon structures. In this effort, a technique that enables complete magnesiothermic reduction of silica to form silicon has been developed. The procedure involves magnesium promoted reduction of vertically oriented mesoporous silica channels on reduced graphene oxides (rGO) sheets. The mesopores play a significant role in effectively enabling magnesium gas to interact with silica through a large number of reaction sites. Utilizing this approach, highly uniform, ca. 10 nm sized silicon nanoparticles are generated without contamination by unreacted silica. The new method for complete magnesiothermic reduction of mesoporous silica approach provides a foundation for the rational design of silicon structures.