We report on the frictional response and atomic process that occur when molecular fluorocarbon molecules of varying lengths are sheared between two polytetrafluoroethylene (PTFE) surfaces. The thicknesses of the molecular layers are also varied. The approach is classical molecular dynamics simulations using a reactive bond-order potential parametrized for fluorocarbons. The results indicate that the presence of the molecules has a significant impact on the measured friction and wear of the surfaces, and that this impact depends on the nature of the fluorocarbon molecules and the thickness of the molecular film. The molecular mechanisms responsible for these differences are presented.