Grazing incidence SAXS (GISAXS) was used to examine the. surface structure of thin Nafion films spin-cast on hydrophobic silanized Si substrate and exposed to water and vapor. GISAXS spectra at low subcritical incidence angles, indicative of a few nanometers thick surface region, showed that in vapor Nafion micelles at the surface tend to align parallel to the surface, while under water they are preferentially oriented normal to the surface, in agreement with previously proposed structural picture and with AFM and contact angle results. However, spectra at near-critical incidence angles representing the bulk of the films indicate the micelles preferentially align normal to the surface, regardless of the external phase. This observation is in contrast with previous studies that employed hydrophilic native Si substrates, in which the observed micelle orientation was parallel to the surface. The proposed explanation assumes that lateral interactions with octadecyl tails and/or heterogeneities at the silanized Si surface, could be responsible for perpendicular alignment in the present case. The heterogeneities could allow preferential interactions of the substrate with both microphases of Nafion, rather than with one microphase, as in the case of bare Si. The observed effect of substrates on micelle orientation suggests an attractive possibility of enhancing transport within Nafion films in a desired direction.