Two polyimides were synthesized for use as alignment layers. The pretilt angles of the liquid crystals, 4-cyano-4'-n-pentylbiphenyl, on the two polyimides were measured by the crystal rotation method. The relative surface atomic concentrations of F/C (%) were measured by Xray photoelectron spectroscopy. Electric force microscopy was utilized to investigate the surface electrostatic property of the two thin polyimide alignment layers before and after rubbing. All results demonstrate that rubbing causes trifluoromethyl moieties to migrate towards the surface, absorb negative charges and orient along the rubbing direction. Thus, it is proposed that distributions of functional groups on the surface of the polyimide after rubbing are anisotropic and the van der Waals forces between the polar groups and liquid crystal molecules play an important role in the uniform orientation of the liquid crystal molecules.