The scanning electrochemical microscope (SECM) in the lithographic mode is used to assess quantitatively, from both theoretical and experimental points of view, the kinetics of irreversible transformation of electroactive molecular moieties immobilized on a surface as self-assembled monolayers (SAMs). The SECM tip allows the generation of an etchant that transforms the surface locally and irreversibly. The resulting surface patterning is detectable by different surface analyses. The quantification of the surface transformation kinetics is deduced from the evolution of the pattern dimensions with the etching time. The special case of slow etching kinetics is presented; it is predicted that the pattern evolution follows the expansion of the etchant at the substrate surface. The case of a chemically unstable etchant is considered. The model is then tested by inspecting the slow reductive patterning of a perfluorinated SAM. Good agreement is found with different independent SECM interrogation modes, depending on the insulating or conducting nature of the covered substrate. The surface transformation measurements are also compared to the reduction of solutions of perfluoroalkanes. The three-orders-of-magnitude-slower electron transfer observed at the immobilized molecules likely describes the large reorganization associated with the generation of a perfluoroalkyl-centered radical anion.