The measurement and optimization of microstructure development in organic semiconductor films is valuable because microstructure in many cases critically impacts electronic performance. We demonstrate a general method to measure microstructure thickness dependence in thin films using surface-sensitive near edge X-ray absorbance fine structure (NEXAFS) spectroscopy. The method is applied to an oligofluorene derivative DDFTTF, which consists of a fluorene-bithiophene-fluorene core that is end-substituted with linear dodecyl groups. The substrate-relative orientations of the aromatic core and the aliphatic end chains are independently determined, and comparing these orientations to terrace heights from atomic force micrographs proves that the end chains are interdigitated or folded. By measuring microstructure development from 6 to 150 nm, we find that DDFTTF exhibits two different preferential microstructures: one with large terraces within which molecules exhibit a strongly vertical orientation, and one with much smaller domains within which molecules exhibit a mildly horizontal orientation. The relative distribution of these two preferential microstructures depends on the distance of the domains from the substrate and the substrate temperature during deposition. The utility of this method is tested using a lamination technique to measure the saturation hole mobility at the top and bottom interface of DDFTTF films. We find that local microstructures with greater pi orbital alignment in the source-drain plane correlate directly to better local saturation hole mobilities.