The nanorelief of orienting surfaces in a nematic layer is studied experimentally. The initial inclination angle of the director and the phase retardation of light in the crystal are determined, and the director reorientation dynamics in the crystal under SB deformation in an electric field is analyzed. It is shown that a thin layer of amorphous hydrogenated carbon (a-C: H) deposited on a GeO monoxide layer with an anisotropic nanorelief produced by the inclined deposition method smoothens the surface topography without changing the surface structure. Modification of the structure and physicochemical properties of the GeO surface alters the conditions of the anisotropic-elastic interaction at the interface with the liquid crystal, as evidenced by an increase in the S-effect threshold and a decrease in the initial inclination of the director from 22° (on the GeO surface) to 0–6°. Strong influence of the surface nanostructure on the dynamics of the director reorientation in the electric field and on the phase modulation of light is experimentally demonstrated. It is shown that the phase retardation of light in the GeO layer covered by an a-C: H film is twice as large as in the layer of the same thickness with a virgin surface.