Investigations exploring the inherent mechanical properties of electronic materials have grown rapidly in recent years largely because they are important in developing flexible electronics, organic displays and sensors. However, our understanding of the mechanical properties of organic semiconductors with a thin-film form remains limited. We report herein on an investigation of the structures and related elastic moduli perpendicular to the surface of a rubrene thin film. A rubrene/Si(100) film typically has a cluster-type morphology mainly comprising crystalline nanodomains within the film. We propose a structural bilayer model that can be used to explain the layered nature or characteristics of the rubrene films. As the film thickness is increased, the enhancement in elastic modulus can be attributed to the presence of a soft surface layer on a hard underlayer. Based on four-point probe measurements, the bilayered nature of such materials can be used to characterize their electrical resistive behavior while interfacial roughness is sensitive to the transport paths of conduction electrons. This information is valuable for future applications of organic semiconductors in flexible devices.