In recent years, Atomic Force Microscope (AFM)-based nanolithography techniques have emerged as a very powerful approach for the machining of countless types of nanostructures. However, the conventional AFM-based nanolithography methods suffer from low efficiency, low rate of patterning, and high complexity of execution. In this frame, we first developed an easy and effective nanopatterning technique, termed Pulse-Atomic Force Lithography (P-AFL), with which we were able to pattern 2.5D nanogrooves on a thin polymer layer. Indeed, for the first time, we patterned nanogrooves with either constant or varying depth profiles, with sub-nanometre resolution, high accuracy, and reproducibility. In this paper, we present the results on the investigation of the effects of P-AFL parameters on 2.5D nanostructures' morphology. We considered three main P-AFL parameters, i.e., the pulse's amplitude (setpoint), the pulses' width, and the distance between the following indentations (step), and we patterned arrays of grooves after a precise and well-established variation of the aforementioned parameters. Optimizing the nanolithography process, in terms of patterning time and nanostructures quality, we realized unconventional shape nanostructures with high accuracy and fidelity. Finally, a scanning electron microscope was used to confirm that P-AFL does not induce any damage on AFM tips used to pattern the nanostructures.