Fourier Transform Infrared and Raman are powerful techniques to evaluate silica and hybrid silica structure. It is possible to evaluate the silica network formation along the hydrolysis and condensation reactions in terms of siloxane rings formation and Si–O(–Si) angle deformation due to the introduction of organic groups, the employed synthetic route or encapsulated species interaction. The siloxane four- or six-membered rings imply in a more rigid or flexible network, respectively, in order to accommodate the organic groups. A structural analysis of the materials is of high importance, since interactions between the encapsulated molecules and the matrix are critical for the device performance, such as sensors. This type of device needs the permeation of an analyte to activate the encapsulated receptor molecules inside the silica structure. Fourier transform infrared spectrometry can be also used to determine parameters of the silica network as a function of the hydrophilicity/hydrophobicity degree and the siloxane ring structure with respect to thin film porosity. This silica structural analysis is reviewed along the text in a tentative of better exploring the data resulting from these powerful techniques. In addition, the functionalization of silica structures by the use of organoalkoxysilanes, which is important to the creation of high-specific materials, can be well described by these two complementary techniques. The Si–C bonds and the maintenance of the organic substituents such as methyl, octyl, octadecyl, vinyl, phenyl, aminopropyl, mercaptopropyl, isocyanatopropyl, iodopropyl, chloropropyl and glicydoxypropyl could be evaluated after the sol-gel synthesis process. The literature regarding silica vibrational spectroscopy is also explored creating a data bank of wave numbers for the most important bonds for different types of silica and hybrid silica materials obtained by different synthetic routes.