Locally rubbing the surface of a polymer using the stylus of an atomic force microscope (AFM nano-rubbing) has recently found extensive applications in prototyping novel micro-and nano-structured liquid crystal (LC) electro-optic devices. We report here on the detailed characteristics of the AFM nano-rubbed polyimide in terms of the friction force and the LC alignment capability. A unidirectionally rubbed polyimide by the contact mode AFM showed anisotropic friction, along and against the rubbing direction, even at a rubbing load as small as 1 nN and yielded a finite pretilt angle reflecting the asymmetry. Rubbing at high loads generated conspicuous scratches on the polyimide surface; when annealed at temperatures well below the glass transition or soaked into an organic solvent, however, these scratches quickly relaxed and completely disappeared while maintaining the capability of aligning LCs. When the load was small, the LC alignment also disappeared altogether. These experimental observations suggest that although the top thin layer might be sufficient to initially orient LCs, persistent surface alignment entails deeper cultivation of anisotropic structures.