We investigated the effects of tunneling current on scanning tunneling microscopy (STM) images of 1-octanethiol (OT) and 1-decanethiol (DT) self-assembled monolayers (SAMs). At a low tunneling current, the domain boundaries and ordered alkanethiol molecules were clearly resolved. As the tunneling current was increased at a constant bias voltage, however, the STM images showed disordered structures of the OT and DT SAMs. As the tunneling current was reduced back to low values, the ordered structures of the alkanethiol molecules reappeared. The reversibility of the process suggests that the sulfur head groups did not rearrange under any of the tunneling current conditions. On the basis of our observations, which are inconsistent with the standard model for STM imaging of molecules on metal surfaces, we consider the STM imaging mechanism in terms of a two-region tunneling junction model.