Chemical force microscopy and related force measurement techniques have emerged as powerful tools for studying fundamental interactions central to understanding adhesion and tribology at the molecular scale. However, detailed interpretation of these interactions requires knowledge of chemical and physical processes occurring in the region of the tip-sample junction that experiments cannot provide, such as atomic-scale motions and distribution of forces. In an effort to address some of these open issues, atomistic molecular dynamics simulations were performed modeling a chemical force microscope stylus covered with a planar C12 alkylthiolate self-assembled monolayer (SAM) interacting with a solid wall. A complete loading - unloading sequence was simulated under conditions of near-constant equilibrium, approximating the case of infinitely slow tip motion. In the absence of the solid wall, the stylus film existed in a fluid state with structural and dynamic properties similar to those of the analogous planar SAM at an elevated temperature. When the wall was brought into contact with the stylus and pressed against it, a series of reversible changes occurred culminating with solidification of the SAM film at the largest compressive force. During loading, the chemical composition of the contact changed, as much of the film's interior was exposed to the wall. At all tip heights, the distribution of forces within the contact zone was uneven and subject to large local fluctuations. Analysis using the Johnson-Kendall-Roberts, Derjaguin-Muller-Toporov, and Hertz contacts mechanics models revealed significant deviations from the simulation results, with the JKR model providing best overall agreement. Some of the discrepancies found would be overlooked in an actual experiment, where, unlike the simulations, contact area is not separately known, possibly producing a misleading or incorrect interpretation of experimental results. These shortcomings may be improved upon by using a model that correctly accounts for the finite thickness of the compliant components and nonlinear elastic effects.