The advancement of molecular nanotechnology requires new tools for the characterization of surface chemical reactivity with nanometer spatial resolution. While spectroscopy on sub-100 nm length scales remains challenging, friction force microscopy (FFM) is a promising tool for the characterization of molecular materials, although to date it has been little used in studies of surface reactivity. Here we report the use of FFM to measure the kinetics of photo-oxidation of self-assembled monolayers (SAMs) of alkanethiols adsorbed on gold surfaces. Two alternative approaches (analysis of friction-load plots and the use of line sections through images of patterned materials) are compared and found to yield data in very good agreement, with rate constants being found to be in good agreement despite being carried out on different microscopes. The use of line-section analysis provides a convenient method for the quantification of the extent of reaction in nanometer-scale patterns created in SAMs by the novel approach of scanning near-field photolithography.