The self-organization of rotaxane thin films into spatially correlated nanostructures is shown to occur upon a thermal stimulus. The mechanism of formation of nanostructures and their organization has been investigated using atomic force microscopy, bright field transmission electron microscopy, selected area electron diffraction, and molecular mechanics simulations. The evolution of the nanostructures follows a complex pathway, where a rotaxane thin film first dewets from the substrate to form nanosized droplets. Droplets coalesce by ripening, generating spatially correlated motifs. In a later stage, the larger droplets change shape, nucleate, and coalesce to yield crystallites that grow into larger crystals by incorporating the surrounding droplets. The results show the following: (i) the nanostructures represent a metastable state of a crystallization process; (ii) spatial correlations emerge during ripening, but they are destroyed as stable nuclei are formed and crystallization proceeds to completion; (iii) crystallization, either on graphite or amorphous carbon films, leads to a precise basal plane, viz. (010), which has minimum surface energy. The inherent degrees of freedom permitted in the rotaxane architecture favors the re-organization and nucleation of the film in the solid state. Low-energy trajectories leading to crystallites with stable surfaces and minimum energy contact plane are found to occur via concerted, small amplitude, internal motions without disruption of packing and intermolecular contacts.