The widespread use of nanotechnology in different application fields, resulting in the integration of nanostructures in a plethora of devices, has addressed the research toward novel and easy-to-setup nanofabrication techniques to realize nanostructures with high spatial resolution and reproducibility. Owing to countless applications in molecular electronics, data storage, nanoelectromechanical, and systems for the Internet of Things, in recent decades, the scientific community has focused on developing methods suitable for nanopattern polymers. To this purpose, Atomic Force Microscopy-based nanolithographic techniques are effective methods that are relatively less complex and inexpensive than equally resolute and accurate techniques, such as Electron Beam lithography and Focused Ion Beam lithography. In this work, we propose an evolution of nanoindentation, named Pulse-Atomic Force Microscopy, to obtain continuous structures with a controlled depth profile, either constant or variable, on a polymer layer. Due to the modulation of the characteristics of voltage pulses fed to the AFM piezo-scanner and distance between nanoindentations, it was possible to indent sample surface with high spatial control and fabricate highly resolved 2.5D nanogrooves. That is the real strength of the proposed technique, as no other technique can achieve similar results in tailor-made graded nanogrooves without the need for additional manufacturing steps.