We have investigated variations in molecularly thin rotaxane films deposited by solvent evaporation, using atomic force microscopy (AFM). Small changes in rotaxane structure result in significant differences in film morphology. The addition of exo-pyridyl moietes to the rotaxane macrocycle results in uniform domains having orientations corresponding to the underlying substrate lattice, while a larger, less symmetric molecule results in a greater lattice mismatch and smaller domain sizes. We have measured differences in film heights both as a function of the solvent of deposition and as a function of surface coverage of rotaxanes. Based on these observations we describe how the use of solvents with higher hydrogen-bond basicity results in films which are more likely to favour sub-molecular motion. (C) 2007 Elsevier B.V. All rights reserved.