It has been demonstrated that it is possible to create laterally differentiated frictional patterning and three-dimensional structures using the Atomic Force Microscope (AFM) probe on the surface of a soft elastic polymer, poly(dimethylsiloxane) (PDMS). The resulting effect of contact mode imaging at low loading forces (< 100 nN), observed in the lateral force mode revealed a homogeneous pattern on the PDMS surface exhibiting higher friction. With higher loading forces (>> 100 nN) the effect is non-uniform resulting in structures with depths on the nanometre scale. The topographic and frictional data revealed stick-slip responses in both the fast (orthogonal to the long axis of the lever) and slow (parallel to the long axis of the lever) directions of probe travel from scanning in a raster pattern. The stick-slip events manifest in the form of a series of shallow channels spaced evenly apart on the polymer surface. Detailed friction loop analysis acquired during the manipulation process showed that the lateral force changed according to the strength of trapping of the tip with the polymer surface exhibiting significant in-plane deformation due to lateral forces being imposed. An incremented increase in the initial loading force resulted in an increase in in-plane displacement and a greater spacing between the stick lines/channels in the slow scan direction. A decrease in channel length in the fast scan direction is also observed as a result of an increase in static friction with normal force, resulting in greater surface deformation and shorter track length for sliding friction.