The effects of film thickness and substrate composition on the ionomer structure in porous electrodes is critical in understanding pathways towards developing higher performance electrochemical devices, including fuel cells and batteries. Insights are gained into the molecular and nanostructural orientation dependence for thin Nafion films (12 to 300 nm thick) on gold, platinum, and SiO 2 model substrates. Molecular orientation is determined from the birefringence measured using spectroscopic ellipsometry, while the nanostructural orientation of the ionic domains was measured using grazing-incidence smallangle X-ray scattering. Density functional theory calculations for the molecular polarizability of the Nafion backbone and side chain show complimentary contributions to the measured birefringence values for the material. Nafion films prepared on SiO 2 substrates exhibit a nearly isotropic molecular and nanostructural orientation. Films on gold and platinum display parallel backbone orientations, relative to the substrate, with decreasing film thickness. However, a birefringence transition towards molecular isotropy is observed for 30 nm thick films on Au and Pt; while the ionic nanostructured domains continuously align parallel to the substrate. This apparent isotropic molecular orientation with increasing domain orientation highlights the difference between the backbone and side chain orientation, a key finding for elucidating transport in confined films at the interfaces.