We investigate by Scanning Force Microscopy the effects of the deposition temperature on the ordering of sexithienyl thin films grown on mica in high-vacuum. The low-temperature aggregates are formed by isotropic grains, while elongated lamellae appears, as the temperature increases which align along directions of the mica lattice. This change in the film morphology does not correspond to a discontinuity in the parameter which describes the anisotropy of the domains, while it makes the slope of the orientational order parameter (2nd Chebyshev polynomial) of the domains to change discontinuously. We infer that the transition is second-order or weak-first order, and we locate the corresponding transition temperature.