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 selforganization at the mesoscopic scale occurs via a nucleationripening 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.bottom-up fabrication ͉ dynamics ͉ rotaxanes ͉ surfaces B ottom-up fabrication requires a hierarchical organization of materials that starts at the molecular level and reaches extended, mesoscopic-length scales. A substantial measure of supramolecular self-organization has already been achieved through specific design and fine-tuning of noncovalent interactions. A variety of supramolecular objects of nanometer size and low dimensionality, such as spheres (1), wires (2), stripes (3), rods (4), toroids (5), and dendrimers (6) have so far been produced. However, self-organization of size-defined objects greater than tens or, more rarely, hundreds of molecules represents a formidable challenge in technologically relevant environments such as surfaces or thin films. On the other hand, a host of organization phenomena at interfaces exhibit spatial correlations across several orders of spatial length scales. Examples are self-affine growth (7), wetting͞dewetting transitions (8), Ostwald ripening (9), spinodal decomposition (10), and breath figures (11). The spatial correlations of these interfacial phenomena, which would be extremely convenient to exploit in fabrication, have diverse origins that range from far-fromequilibrium growth conditions, to the presence of metastability, to the competition between intermolecular and surface interactions. Indeed, if possible, one would want to combine the supramolecular and the interfacial organization to obtain a deterministic assembly, where spatial correlations exist from a few molecular objects to mesoscopic constructs.Our aim was to find suitable molecular systems that would not stay steadily ''anchored'' to a surface but, instead, upon an external stimulus, would change the pattern of interactions, thereby providing the input for long-scale reorganization. This is the case of rotaxane thin films that self-organize into patterns of dots upon a thermal treatment (12).Rotaxanes consist of a macrocycle (molecular ring) mechanically interlocked with a dumbbell (13). Their dynamical properties (14, 15) have heralded them as attractive systems for a number of applications that include molecular switches (16, 17), nanorecording (18), and protection of electroluminescent emitters (19). Earlier, we have shown that films of three rotaxanes, stimulated locally with the tip of an a...