Nowadays, mechanical AFM-based nanolithography has emerged as the most promising nanolithography technique, allowing the patterning of nanostructures on polymer layers with a sub-nanometer resolution. In such a stimulating context, we developed the Pulse-AFM method to obtain continuous structures with a controlled depth profile, either constant or variable, on a polymer layer. However, those nanostructures are contoured by polymer pile-ups that limit their integration into high-tech devices. Since pile-up removal is still an open challenge, AFM force–distance curve analysis was performed to characterize the stiffness of bulges, and an effective strategy to easily remove pile-ups while preserving the shape and morphology of nanostructures was then developed.