We have determined by atomic force microscopy the average roughness of substrates covered with a different indium tin oxide (ITO) thickness. We have found that the higher the ITO thickness is the higher the roughness. Then, the preferential alignment of liquid crystalline mixtures, formed by a low molecular weight liquid crystal and a liquid crystalline monomer, on such substrates has been investigated, Samples have turned out to be homeotropically aligned by surface interactions. These cells have been UV irradiated in order to achieve the photo-polymerization of the liquid crystalline monomer. We have found that rougher surfaces are able to store the homeotropic alignment in the anisotropic polymer matrix. The order degree of polymerized films has been estimated as a function of liquid crystal content.