Scanning tunneling (STM) and atomic force (AFM) microscopies have been used to examine structural features of monolayers formed from the spontaneous adsorption of alkanethiols at Au(111) surfaces. In addition to the atomic scale spacings of the adlayer, the depressional features found in both large (50-250 nm) and atomic scale images have been characterized for monolayers formed from several alkyl chain lengths. These depressions, which are more predominant at monolayers from long chain alkanethiols, appear as 2-4 nm diameter, 0.24 nm deep depressions in STM images and as 2-5 nm diameter, low frictional features in lateral force images. The lateral force images of these depressions, along with an explanation of the imaging mechanism, are presented for the first time. Atomic scale STM images reveal the presence of the adlayer lattice within the depressions. In addition, atomic scale images show that these depressions occur along visible domain boundaries. Together, our results indicate that these depressions originate in the topmost layer of the Au(111) surface and are not a consequence of structural inhomogeneities in the monolayer or of imaging artifacts. Based on these findings, a mechanism for the origin of the depressions is proposed.