A mechanistic picture of the effects of rubbing on polyimide alignment layer (AL) surfaces and nematic liquid crystal (LC) pretilt angles (ΘP), leading to establishing a mechanism of determination of ΘP’s, was proposed on the basis of the study of the change in surface polarity of a polyimide AL with the rubbing force and density, and the subsequent changes in the ΘP and the azimuthal anchoring energy. In the regime of relatively weak rubbing where inhomogeneous, patchy surface modification (the microscopic reorientation of polymer functional groups and the orientation of polymer backbones) occurs, the surface polarity, the anchoring energy, and the ΘP all increase monotonically with rubbing strength. These increases correlate to an increase in the area fraction of the reoriented/oriented AL surface which generates in-plane orientation of the first LC monolayer at the surface and subsequently bulk alignment. Beyond this region in which the AL surface gets modified sufficiently to induce fully developed in-plane orientation of the LC monolayer, the surface chemistry and roughness have dominant effects on the ΘP and the anchoring energy. The increase in surface polarity and the generation of a larger reoriented surface area by high-force rubbing, which enhances the attractive interaction between the LC monolayer and the rubbed surface, contribute to increases in both the anchoring energy and the thermal stability of ΘP and to a decrease of ΘP. This decrease of ΘP with increasing AL surface polarity was verified by studying the relationship between ΘP and surface polarity under constant rubbing conditions by manipulating the surface polarity via the degree of imidization of a poly(amic acid) AL.