Rubbing-induced surface reconstruction of the polyimide poly(biphenyl dianhydride-p-phenylenediamine) (BPDA-PDA), in the form of 5-300 nm thin films supported on silicon substrates, has been studied using high-precision polarized infrared vibrational spectroscopy in conjunction with spectral simulations. Under unidirectional rubbing, a reversible, selective reorientation of domains of initially well-ordered chains is observed, with the amount of reoriented material equivalent to an similar to 1-3 nm thick surface layer, independent of the total film thickness. Accompanying this process are extensive perturbations of the imide ring structures, which include bond distortions of the [O=C-N-C=O] units and out-of-plane rotation of the rings around the chain axis, effectively causing a molecular-scale roughening along the aligned chain axes while maintaining the periodic repeat unit spacing. These effects are proposed to arise from dynamic chain-chain steric interactions that occur as chains align under the applied buffing force. An analogous bulk behavior is shown for the molecular response of unsupported BPDA-PDA films to uniaxial tensile strain. These data provide a new description of the buffed BPDA-PDA polymer surface and thus provide an improved basis for understanding the mechanism of liquid crystal alignment on these surfaces.