Silica films under present reactive electron beam deposition conditions have depicted a novel self-organized surface grain structures when probed through atomic force microscopy, 2D fast Fourier transform and glancing incidence Xray diffraction techniques. The formation of such ordered surface grain structures is observed to be strongly correlated to the nucleation and growth process of the silica films. However, the nature of the substrate (amorphous or crystalline) and multilayer geometries have influenced the shapes, sizes and abundances in the grain structures and the ordering. The strain mediation of such ordered structures when buried under polycrystalline layers like Gd₂O₃ have shown to influence both the grain size as well as roughness. A variety of grain structure evolutions and morphological changes in silica layers were noticed in different multilayer geometries. It is, hence, inferred that by appropriately using combinations of these materials, it is possible to have a control over the multilayer morphology and grain structures, which is a very relevant factor in developing precision ultraviolet laser coatings.