The study of solid-fluid transitions in fluorinated ionic liquids using differential scanning calorimetry, rheology, and molecular modeling techniques is an essential step toward the understanding of their dynamics and the thermodynamics and the development of potential applications. Two fluorinated ionic liquids were studied: 1-hexyl-3-methylimidazolium perfluorobutanesulfonate, HMIm(PFBu)SO3, and tetrabutylammonium perfluorobutanesulfonate, NB4(PFBu)SO3. The experimental calorimetric and rheological data were analyzed taking into account the possible mesoscale structure of the two fluorinated ionic liquids. The simulation results indicate the possible formation of three nanosegregated domains-polar, nonpolar, and fluorous-that may have a profound impact on ionic liquid research. In the case of HMIm (PFBu)SO3 the three types of mesoscopic domains can act as interchangeable jigsaw pieces enabling the formation of multiple types of crystals and inducing the observed calorimetry and rheological trends.