Understanding the relationship between elastic, chemical, and thermal properties is essential for the prevention of the behavior of SiO2 flint aggregates during their application. In fact, the elastic properties of silica depend on chemical and heat treatment. In order to identify the crystallite sizes for natural SiO2 before and after chemical treatment samples, Williamson–Hall plots and Scherer’s formulas are used. The silica nanofibers obtained and their microstructure changes under thermal and chemical treatment are characterized using different techniques (XRD, VP-SEM, TEM, FTIR, TDA, and TGA). Both the strains (ε) and the crystallite sizes (DW–H) are obtained from the slope and from the βcosθ-intercept of a graph, respectively. The crystalline quality is improved upon heating, as shown by the decrease in the FWHM of the SiO2(101) peaks, which is confirmed by Fourier transform infrared spectroscopy (FTIR). The microstrain estimated at 1.50 × 10−4 units for natural SiO2 is smaller than that for SiO2 after chemical attack which is estimated at 2.01 × 10−4 units. Based on the obtained results, SiO2 characterized with controlled micromechanical, thermal, and chemical properties may be used as a filler to improve the performance properties of the strength, microstructure, and durability of some composites.