We synthesized two polyimides (PIs), poly(4,4'-(9,9-fluorenyl) diphenylene cyclobutanyltetracarboximide) (CBDA-FDA) and poly(4,4'-(9,9-fluorenyl) diphenylene pyromellitimide) (PMDA-FDA), and investigated in detail the surface morphology, molecular orientation, and nematic liquid crystal (LC) alignments of rubbed CBDA-FDA and PMDA-FDA films. The rubbed CBDA-FDA film surface was found to contain microgrooves that run parallel to the rubbing direction, but was found to induce LC alignment perpendicular to the rubbing direction. In contrast, the rubbed PMDA-FDA film surface was found to contain unusual meandering microgrooves that run perpendicular to the rubbing direction; this is the first report of such structures on a rubbed PI film. The PMDA-FDA film surface was found to induce LC alignment parallel to the rubbing direction. Even though these two PI films have quite different groove structures and LC alignment behaviors, the polymer main chains in their surfaces lie in the film plane and are preferentially oriented along the rubbing direction, and the fluorenyl side groups lie in the out-of-plane and are preferentially oriented perpendicular to the rubbing direction. These LC alignment, anchoring energy, surface morphology, and polymer segmental orientation results indicate that LC alignments on the surfaces of rubbed PI films are determined by the interplay between the directionally anisotropic interactions of the LC molecules with the oriented polymer main chain segments, the oriented fluorenyl side groups, and the microgrooves. The directionally anisotropic interactions of the LC molecules with the oriented polymer chain segments were found to be much stronger than those with the directionally developed microgrooves. We conclude that CBDA-FDA and PMDA-FDA PIs are promising alignment layer materials for the fabrication of advanced LC display devices.