Barrier height of self-assembled monolayers (SAMs) on Au(111) was measured using scanning tunneling microscopy (STM) with a vertical modulation. We obtained nanometer scale STM images of alkanethiol SAMs, and binary component SAM films fabricated by an implantation technique. Local barrier height on the alkanethiol SAM at the depressions and the domain boundaries is larger than that on the domains where the molecular lattice is visible, probably due to the molecular density or orientation. A molecular resolution contrast was obtained at a conjugated molecule embedded in the alkanethiol SAM, reflecting the difference in the molecular species. We found that the tip-sample interaction force affects the barrier height measurements, especially when the tunneling gap is small, e.g., on nonanethiol SAM at the tunneling resistance smaller than 50 GΩ.