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The choice of deposition technique and post deposition treatment can significantly influence the performance of organic electronic devices by altering the complex relationship between film properties and charge transport. Herein, the influence of deposition method and post deposition thermal annealing on the thin‐film properties of an emerging semiconductor, bis(tri‐n‐propylsilyl oxide) SiPc ((3PS)2‐SiPc), is examined by polarized Raman microscopy. Comparing physical vapor deposition (PVD) and spin‐coating, the orientation of (3PS)2‐SiPc molecules in films is determined and further characterized by X‐ray diffraction to assess variations in microstructure and morphology due to thermal annealing. Despite differences in film formation, non‐annealed organic thin‐film transistors (OTFTs) fabricated by PVD and spin‐coating resulted in similar electron mobilities (μe) on the order of 10−2 cm2 V−1 s−1 and threshold voltages (VT) of 10–20 V. Films fabricated by PVD annealed at 175 °C transition to a new polymorphic form with molecules aligned at a higher angle to the substrate and exhibiting reduced device performance. Conversely, spin‐coated films do not undergo any new polymorph formation or structural reorganization with thermal annealing. PVD fabricated films are thus more readily able to undergo transformations to structure and morphology with post deposition processing, while the microstructure of spin‐coated films is established at the time of deposition.