Fluorinated ionic liquids (FILs) are growing into greener biomaterials for engineering applications due to their exceptional physicochemical properties, such as their vanishing vapour pressure, solvent quality, outstanding chemical and biological inertness, null flammability, low surface tension, high surfactant power and high thermal stability. Tuning these properties by the proper choice of cations and anions also plays an important role in controlling the distinct types of interactions, namely van der Waals, hydrogen bonds and coloumbic. Moreover, the novel FILs herein proposed present an interesting nanostructuring effect, promoting the appearance of a third nanosegregated domain (fluorous), which permits control of their segregation capacity, converting FILs into 3-in-1 solvents with enhanced solubilisation power. Adjusting the different types of interactions, the size and type of domains (polar, hydrogenated/fluorinated apolar), surfactant behaviour and the solubility in water and other fluids will provide the ingredients needed to use these FILs as biomaterials in different applications where fluorocarbon compounds display some handicaps. This chapter provides a critical review of the characteristic and complex behaviour of this family of ionic liquids and their possible applications. The attained results will have a clear impact on applications using fluorocarbon compounds and ionic liquids.