When a local mechanical perturbation is applied to the surface of a thin film of a mechanically interlocked molecule (a rotaxane), the molecules self-organize into periodic arrays of discrete dots or lines. The dimensionality of the nanostructures depends on whether the mechanical stimulus acts along a 1D line or over a 2D area. The size (50-500 nm) and periodicity (100-600 nm) of the patterns are controlled solely by the film thickness. This self-organization at the mesoscopic scale occurs via a nucleation-ripening mechanism eased by the relatively low energy barriers of the intramolecular rearrangement introduced by the mechanical bond. The phenomenon can be exploited as a bottom-up nanofabrication method.