The neutral cluster beam deposition (NCBD) method has been applied to produce and characterize organic thin-film transistors (OTFTs) based upon tetracene and pentacene molecules as active layers. Organic thin films were prepared by the NCBD method on hexamethyldisilazane (HMDS)-untreated and -pretreated silicon dioxide (SiO2) substrates at room temperature. The surface morphology and structures for the tetracene and pentacene thin films were examined by atomic force microscopy (AFM) and X-ray diffraction (XRD). The measurements demonstrate that the weakly bound and highly directional neutral cluster beams are efficient in producing high-quality single-crystalline thin films with uniform, smooth surfaces and that SiO2 surface treatment with HMDS enhances the crystallinity of the pentacene thin-film phase. Tetracene- and pentacene-based OTFTs with the top-contact structure showed typical source-drain current modulation behavior with different gate voltages. Device parameters such as hole carrier mobility, current on/off ratio, threshold voltage, and subthreshold slope have been derived from the current-voltage characteristics together with the effects of surface treatment with HMDS. In particular, the high field-effect room-temperature mobilities for the HMDS-untreated OTFTs are found to be comparable to the most widely reported values for the respective untreated tetracene and pentacene thin-film transistors. The device performance strongly correlates with the surface morphology, and the structural properties of the organic thin films are discussed.