Scanning tunneling microscopy (STM) images of a self-assembled alkanethiol monolayer film on gold show a structure that contains flat areas with pits. An important characteristic of these pits, and one which has been a subject of interest in the recent literature, is their depth. For instances in which the measured depth is comparable to a single atomic step height of the gold substrate, the pits have been assigned as monolayer-deep defects in the gold substrate, covered by alkanethiol molecules. For instances in which the measured depth is greater than a single atomic step height of gold, the pits have been assigned as defects in the alkanethiol monolayer itself Since the diameters of those pits are small and the tips used for scanning probe microscopy (SPM) imaging have a finite radius, it is possible that the structural interaction between the tip and surface prevents SPM from measuring the true depth of the pits in most cases. In this study, we construct a model to understand this phenomenon quantitatively, and analyze the measured depth of the pits. STM images of self-assembled octadecanethiol/Au(111) from the same surface but obtained with tips of different sizes are presented. We show that in some STM images the apparent depth of the pits is coincidently comparable with the single atomic step height of the gold substrate surface. In other images we show that the true depth of the pit is measured, and that it is interpreted as the thickness of an octadecanethiol monolayer (approximately 25.3 +/- 0.5 angstrom).