Vibrational sum frequency generation (VSFG) spectroscopy was used in conjunction with steady-state IR spectroscopy, atomic force microscopy (AFM), and spectroscopic ellipsometry to characterize organic semiconductor thin films that were vapor deposited on silica- and trimethoxy(octadecyl)silane (ODTMS)-functionalized silica surfaces. The growth of perylene derivative N,N′-dioctyl-3,4,9,10-perylenedicarboximide (PTCDI-C8) was found to proceed differently on simple glass slides relative to that of native oxide on silicon and fused quartz slides. VSFG was applied to these samples to isolate structural changes that occurred specifically at the buried interface between the organic semiconductor and the silica dielectric upon thermal annealing. A model was introduced to globally fit the imide carbonyl symmetric and asymmetric interfacial spectra that included contributions from both inner and outer interfaces. The fits to the VSFG data and AFM topographic images revealed significant reordering at the outer interface on all substrates upon thermal annealing. Within the model, the spectroscopic data reported that the inner interfacial PTCDI-C8 monolayer reoriented to a more reclined phase on bare substrates after annealing but remained essentially unchanged on ODTMS monolayers. Electrical characterization of PTCDI-C8 field-effect transistors indicated that electron mobilities were higher on bare substrate devices but could be improved by a factor of 2 on both surface types by thermal annealing. The mobility effects were attributed to the annealing-driven coalescence of PTCDI-C8 grain boundaries. Consistent with previous structural reports, the molecular rearrangements of the first monolayer of PTCDI-C8 on bare substrates that were reported by VSFG spectroscopy had a noticeable impact on the device performance.