In the past decade, scanning tunneling microscopy (STM) has revealed new information regarding self-assembled monolayers (SAMs) of organothiols on Au(111) at the molecular level. The periodicity, defects, morphology, and various phases during the self-assembly process have been visualized with unprecedented detail. Using STM under ultrahigh vacuum, new insights regarding SAMs have been revealed from the perspective of potential applications in molecular devices. This article focuses on a molecular-level understanding of the formation of adatom and vacancy islands and reveals how the structure is impacted by introducing aromatic termini. The thermal stability and thermally induced structural evolution of SAMs are monitored in situ. The behavior of alkanethiol molecules under local electric field and tunneling current are studied with molecular resolution. Molecular-level insight regarding negative differential resistance of SAMs is also discussed.