Recent developments of nanostructured coatings have reached a point where extensive investigations within multi-layer systems are necessary for further implementation in novel photonic systems. Although sculptured thin films are explored for decades, no optical and structural measurements have been performed for anisotropic nanostructured multi-layer coatings with different deposition conditions of the dense layer. In this paper, we present extensive morphological analysis on silica nanostructured anisotropic films. Changing the deposition angle from 66° to 84°, indicate the changes in surface filling from 84\% to 57\%, respectively, while phase retardance has a maximal value of 0.032°/nm at 70° and 72° angles. We also present the investigation of covering such structures with the dense layer at different conditions. As a result, the technology for maintaining initial anisotropic properties is developed for extending spectral difference 1.6 times and phase retardation by 5\% in anisotropic multi-layer coatings. Furthermore, we present simulations of growing silica layer using experimental conditions in the Virtual Coater framework resulting in virtual anisotropic films for comparison with measurements. The minimal impact on the anisotropy of porous layer is reached with the deposition of dense layer at 30° angle during constant substrate rotation.