The performance of bottom-contact thin-film transistor (TFT) structures lags behind that of top-contact structures owing to the far greater contact resistance. The major sources of the contact resistance in bottom-contact TFTs are believed to reflect a combination of non-optimal semiconductor growth morphology on the metallic contact surface and the limited available charge injection area versus top-contact geometries. As a part of an effort to understand the sources of high charge injection barriers in n-channel TFTs, the influence of thiol metal contact treatment on the molecular-level structures of such interfaces is investigated using hexamethyldisilazane (HMDS)-treated SiO2 gate dielectrics. The focus is on the self-assembled monolayer (SAM) contact surface treatment methods for bottom-contact TFTs based on two archetypical n-type semiconductors, α,ω-diperfluorohexylquarterthiophene (DFH-4T) and N,N′bis(n-octyl)-dicyanoperylene-3,4:9,10-bis(dicarboximide) (PDI-8CN2). TFT performance can be greatly enhanced, to the level of the top contact device performance in terms of mobility, on/off ratio, and contact resistance. To analyze the molecular-level film structural changes arising from the contact surface treatment, surface morphologies are characterized by atomic force microscopy (AFM) and scanning tunneling microscopy (STM). The high-resolution STM images show that the growth orientation of the semiconductor molecules at the gold/SAM/semiconductor interface preserves the molecular long axis orientation along the substrate normal. As a result, the film microstructure is well-organized for charge transport in the interfacial region.