Deviation from a perfect 2D-hexagonal (p6m) structure, for CTAB-silica mesostructured films prepared by adding different amounts of excess ethanol to a solution of CTAB and TEOS just before spin coating on OH- and H-terminated Si substrates, is observed from combined X-ray reflectivity and grazing incidence small angle X-ray scattering measurements. Such a deviation can be well understood in terms of the shape and ordering of the micelles, with or without the silica coating layer's contribution, inside the film. For example, cylindrical shaped micelles, which are initially circular on a hydrophilic OH-terminated Si substrate in order to form a perfect 2D-hexagonal structure, become elliptical (extended along the in-plane) on a hydrophobic H-terminated Si substrate to form a slightly compressed 2D-hexagonal structure due to a different attachment of the film to the substrate. With time, due to the drying of the silica materials and its restricted movement along the in-plane direction, the films on both the substrates are compressed along the out-of-plane direction only, to form observed centered rectangular (c2mm) structures. Also, due to the asymmetric shrinkage, stress is developed, which deteriorates the ordering in the film. The final shape of the micelles, including the silica coating layer's contribution, shows maximum and minimum deviations from the circular shape inside the thick film on a OH-Si substrate and the thin film on a H-Si substrate, respectively. The deviation in the shape of the micelles itself, which is of actual importance, seems to be maximum and minimum inside the thick film on a H-Si substrate and the thin film on a OH-Si substrate, respectively, and is essentially determined by the substrate nature and initial silica wall thickness.