The surface relationship between the orientation structure of liquid crystal molecules and the polymeric alignment layer was investigated by a slit-flow viscometer. In this study, an experimental determination is described for the direct measurement of the anisotropic viscosities of liquid crystals without a magnetic field. In addition, the effects on apparent viscosity for nematic and smectic liquid crystals caused by various rubbing depths on the alignment layer, and the gap dependence of apparent viscosity for smectic liquid crystals were also investigated. With increasing rubbing depth, the apparent viscosity of nematic liquid crystals on both parallel and perpendicular orientations becomes higher. And the apparent viscosity of smectic liquid crystals also becomes higher on parallel orientation, but becomes lower on perpendicular orientation. Furthermore, the rubbed surface of the alignment layer was observed using an atomic force microscope (AFM), and the orientation structures of smectic liquid crystals in the slit cell were elucidated.