Scanning probe lithography (SPL) appears to be a reliable alternative to the use of masks in traditional lithography techniques as it offers the possibility of directly producing specific chemical functionalities with nanoscale spatial control. We have recently extend the range of applications of catalytic SPL (cSPL) by introducing a homogeneous catalyst immobilized on the apex of a scanning probe. Here we investigate the importance of atomic force microscopy (AFM) physical parameters (applied force, writing speed, and interline distance) on the resultant chemical activity in this cSPL methodology through the direct topographic observation of nanostructured surfaces. Indeed, an alkene-terminated self-assembled monolayer (alkene-SAM) on a silicon wafer was locally epoxidized using a scanning probe tip with a covalently grafted manganese complex bearing the 1,4,7-triazacyclononane macrocycle as the ligand. In a post-transformation process, N-octylpiperazine was covalently grafted to the surface via a selective nucleophilic ring-opening reaction. With this procedure, we could write various patterns on the surface with high spatial control. The catalytic AFM probe thus appears to be very robust because a total area close to 500 μm2 was patterned without any noticeable loss of catalytic activity. Finally, this methodology allowed us to reach a lower lateral line resolution down to 40 nm, thus being competitive and complementary to the other nanolithographical techniques for the nanostructuration of surfaces