In recent decades, great efforts have been made to develop innovative, effective, and accurate nanofabrication techniques stimulated by the growing demand for nanostructures. Nowadays, mechanical tip-based emerged as the most promising nanolithography technique, allowing the pattern of nanostructures with a sub-nanometer resolution, high reproducibility, and accuracy. Unfortunately, these nanostructures result in contoured pile-ups that could limit their use and future integration into high-tech devices. The removal of pile-ups is still an open challenge. In this perspective, two different AFM-based approaches, i.e., Force Modulation Mode imaging and force-distance curve analysis, were used to characterize the structure of pile-ups at the edges of nanogrooves patterned on PMMA substrate by means of Pulse-Atomic Force Lithography. Our experimental results showed that the material in pile-ups was less stiff than the pristine polymer. Based on this evidence, we have developed an effective strategy to easily remove pile-ups, preserving the shape and the morphology of nanostructures.