Ordered mesoporous silica micrometer-sized structures have been fabricated via selective dewetting of the coating sol on a hydrophilic/hydrophobic fluorinated silica substrate, which had been pre-patterned using deep X-ray lithography with a synchrotron radiation source. We have observed that deposition of mesoporous films on the pre-patterned areas can be used as a design tool for obtaining regions of specific geometry and dimensions. The evaporation of the solution in constrained conditions because of pinning at the pattern edges gives layers with thicker edges. This edge effect appears dependent upon the dimension of the pre-patterned hydrophilic/hydrophobic layer; in smaller patterns, the evaporation is too fast and thickening of the edges is not observed. We have used infrared imaging, optical profilometry, and atomic force microscopy to characterize the patterned layers and the edge effect, produced by pinning at the border of the microstructures.