We report the results of a direct comparison of the adhesion, friction, and mechanical properties between alkanethiol self-assembled monolayer films terminated by either CH3 or CF3 end groups using both interfacial force (IFM) and atomic force (AFM) microscopies. The purpose of this work is to gain insight into the detailed origins of the differing frictional behavior previously observed with AFM. The IFM results reveal an increased adhesive interaction for the CF3-terminated film due to the highly polar nature of the end groups. In agreement with earlier studies, the AFM results show two linear regions with differing frictional slopes for the CH3-terminated film but only a single slope for the CF3-terminated film. We contrast the differences between these techniques, similar to 100 times smaller tips for the AFM, and discuss the role of the mechanical properties, the increased adhesive interaction, and the amount of disorder present in the film in creating differences in frictional behavior between the two systems. We conclude that increased adhesion for the CF3-terminated film plays an important role in the observed differences in frictional behavior, while the differences between the two techniques can be traced to the different tip sizes and the consequent responses to the presence of disorder in the films.