The nature of the "holes" in self-assembled thiol monolayers-found in previous scanning-tunneling microscopy (STM) studies-is elucidated using STM with unprecedented high tunneling resistances (up to 1 TOMEGA). This enables the nondestructive imaging of dodecanethiol monolayers on Au(111) with atomic-scale resolution. The molecules are found to order in square-root 3 x square-root 3 domains separated by different types of missing row structures. This molecular ordering is typical not only for terraces but also for regions within "holes". These regions are therefore neither openings (pinholes) nor regions of disorder in the monolayer. Instead, they are attributes of the Au surface, which most likely originate from an etching process during the adsorption of the molecules.