Polymer coated substrates modified both by mechanical rubbing and optical buffing have been found to cause liquid crystal molecules to align. Atomic force microscopy (AFM) was used to characterize the differences and similarities in polyimide substrate coatings after being subjected to these two processes. Though the buffing processes caused similar alignment on the surfaces, it was found that the mechanical rubbing created grooves on the order of 250nm, whereas optical buffing resulted in no changes to topographic structure on the order of 100nm scale and some variations at smaller scales. From this observation it was confirmed that the interaction causing the alignment must be associated with molecular alignment rather than large scale physical grooving.