Molybdenum disulfide (MoS2) is a transition-metal dichalcogenide with many applications including in electronic devices and sensors. A critical issue in the development of these devices is the high resistance between the metal contact and the molybdenum disulfide layer. In this study, we employ Raman spectroscopy and X-ray photoelectron spectroscopy to investigate the modification of Au-MoS2 contact properties using functionalized alkanethiolate self-assembled monolayers (SAMs). We demonstrate that both 2H and IT MoS2 strongly interact with the underlying Au substrate. The electronic properties of the interface are mediated by the dipole moment of the alkanethiolate SAM, which have a -CH3, -CO2C6F5, -OH, or -COOH terminal group. Finally, we demonstrate the site-selective deposition of 2H and IT MoS2 on micropatterned SAMs to form conducting-semiconducting patterned MoS2 films.