Self-assembled monolayers (SAMs) of alkanethiols on Au(111) have been of great interest for decades. The formation of thiol-based SAMs on Au(111) has been of particular interest due to their ease of formation and tunability. The advent of the scanning tunneling microscope (STM) has allowed scientists to further their understanding of the mechanisms by which SAMs form. While much research has been done on SAMs and how they form, there is still much to be discovered. In this thesis, the diffusion of three different SAM coated Au(111) samples were studied via STM. The first project focuses on a two-dimensional gas phase of the molecules which prevented immobilization of the gold surface. The factors potentially affecting the rate of decay of the various samples are also discussed. The second project discusses preliminary results into how STM scanning current affects octanethiol monolayers. Generally, a higher tunneling current results in more molecular motion on the surface.