The non-contact atomic force microscopy (nc-AFM) images of the single alkanethiolate molecules embedded in the bicyclo[2,2,2]octylmethylthiolate (BCO) self-assembled monolayer (SAM) are simulated using the all-atom empirical force field model. The tip is modeled by the chemically inactive and unpolarized carbon nanocone apex. When the alkyl chain is longer than the BCO matrix, the protruded chain is observed to be lower than its actual height. Even if the alkyl chain has a similar height to the BCO, the former is observed to be slightly lower than the latter. These findings indicate that even when the chemical and electrostatic interactions are not relevant for imaging, the nc-AFM images do not always give true topographical information of the molecules under the tip. [DOI: 10.1380/ejssnt.2006.299]