This study investigates controlled micro/nano manipulation of PDMS using scanning probe microscopy (SPM). Lithographic results revealed stick-slip phenomena in both the fast and slow scan directions, verified with the aid of friction loop analysis. Varying the normal loading force, scan speed and resolution allowed the control of certain lithographic outcomes e.g., spacing and depth of troughs, and the dynamic stick-slip amplitude. The PDMS surface experienced significant in-plane deformation in response to the tip-induced lateral force. This displacement increased with increasing loading force, creating greater spacing between troughs in the slow scan direction. Simultaneous generation of a lateral displacement in the fast scan direction caused a decrease in trough length with increasing loading force due to an increase in static friction with normal force, resulting in a greater surfaces relaxation, and shorter track length of dynamic friction.