Nanoporous and nanowire structures based on silicon (Si) have a well recognized potential in a number of applications such as photovoltaics, energy storage and thermoelectricity. The immiscibility of Si and aluminum (Al) may be utilized to produce a thin film of vertically aligned Al nanowires of 5 nm diameter within an amorphous silicon matrix (a-Si), providing a cheap and scalable fabrication method for sub 5 nm size Si nanostructures. In this work we study functionalization of these structures by removal of the Al nanowires. The nanowires have been etched by an aqueous solution of HCl, which results in a structure of vertically aligned nanochannels in a-Si with admixture of SiO x . The removal of Al nanowires has been monitored by several electron microscopy techniques, x-ray diffraction, Rutherford backscattering spectroscopy, and optical reflectance. We have established that optical reflectance measurements can reliably identify the complete removal of Al, confirmed by other techniques. This provides a robust and relatively simple method for controlling the nano-fabrication process on a macroscopic scale.