In this work, a structural characterization of sputtered silica films was carried out using Raman spectroscopy. Due to the low cross-section and the thinness of the silica layer, its Raman signature is dwarfed by that of the glass substrate and is therefore difficult to extract. Overcoming these limitations represents an experimental challenge and requires the development of specific analysis strategies. For this purpose, an integrated approach for extracting and interpreting the Raman signature of amorphous silica films deposited on a soda-lime glass substrate was developed, based on three distinct methods: delamination of the sputtered silica film, creating a reflective mask substrate by depositing a metallic silver coating on the glass substrate and applying a numerical signal analysis (Non-negative matrix factorization) to the multidimensional dataset acquired through depth profile acquisitions on silica films directly deposited on a glass substrate. The reliability of each proposed method is demonstrated for the extraction of the silica thin film Raman spectra. These various methods can be easily extended to other materials, either crystalline or amorphous. Furthermore, we discuss the advantages and the limits of each approach. Applying this methodology allowed us to highlight the structural differences between sputtered silica thin film and bulk vitreous silica glass (v-SiO2). Magnetron sputtering film deposition is shown to form dense silica glass layers, with an estimated densification ratio, measured by x-ray reflectivity, equal to 7%. At the medium distance range, the network connectivity change in v-SiO2 is expressed by an unusually high population of three-membered rings leading to a more compact structure. The short-range order transformation was also studied by deriving the intertetrahedral angle decrease. The present results could be a step towards advanced investigation to gain insights into the structure of films at the atomic level.