Orientational ordering within nanoscale (70-8 nm) thickness fluorinated ionomer films on Si substrates was investigated through the use of attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy in conjunction with electromagnetic field calculations. A spectral model was developed for Nafion thin films across the 1400-950 cm-1 region from frequency-dependent, isotropic optical constants derived from Kramers-Kronig analysis of ionomer transmission infrared spectra. The model considered infrared light propagation within the parallel boundary regions between the Ge ATR crystal, the ionomer film, and the Si substrate supporting the film. The calculations reproduced overall polymer thickness-dependent changes in peak frequencies and band shapes observed in experimental spectra recorded with p- and s-polarized light. General trends were traceable to effects of anomalous dispersion and electric field enhancement within the nanoscale gap separating the Ge and Si phases. However, optical effects could not fully explain perturbations in spectra of the thinnest films, where molecular orientational ordering is expected to be strongest. Strategies for gleaning further molecular structural detail from vibrational spectra of ultrathin (<50 nm) ionomer films are discussed.