The possibility to control the assembly of molecules on a given substrate is particularly important for polymeric systems. Self-assembly of polymer chains on a substrate can be controlled by modifying selectively the chemistry of the substrate surface and/or the polymer itself in order to create patterned polymer films with tailored length scales. A novel tool to change the polymer morphology in order to achieve the requested superficial structures and textures is the atomic force microscopy (AFM). In this paper, we shall demonstrate how to obtain ordered ripple structures induced by an AFM tip on a polymer thin film. It is well known that a polymer surface scanned by a probe tip can change its morphology assuming typical ripple structures. These structures however are expected to be formed for high applied loads (>10 nN) and after many scanning cycles (>10). On the contrary, we shall show how to obtain the ripple formation just by a single AFM scan and for relatively low applied loads. Such ripple structures can be modulated and modified by changing the applied load, scanning velocity and angle. In this way, it is possible to obtain sinusoidal structures with suitable amplitude, periodicity and orientation. Beyond the general contribution to the development of nanolithography, the patterns obtained by this method can find many applications in biomaterial polymer science (such as scaffolds for cell proliferation in tissue engineering).