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A comparative study on alignment performance and microstructure of inorganic layers used for liquid crystal cell conditioning has been carried out. The study has focused on two specific materials, SiO
x
and SiO
2
, deposited under different conditions. The purpose was to establish a relationship between layer microstructure and liquid crystal alignment. The surface morphology has been studied by FESEM and AFM. An analysis on liquid crystal alignment, pretilt angle, response time, contrast ratio and the conditions to develop backflow effect (significant rise time increase due to pure homeotropic alignment) on vertically-aligned nematic cells has been carried out. A technique to overcome the presence of backflow has been identified. The full comparative study of SiO
x
and SiO
2
layer properties and their influence over liquid crystal alignment and electrooptic response is presented.