Thin hybrid films of the organic fullerenes and inorganic (metallic) transition metals have been synthesized, and their specific structural forms inspected. Using the IBA analytical technique (mainly Rutherford Backscattering / Channeling), and other complementary methods (e.g., micro-Raman spectroscopy), nanostructures of the hybrid materials have been studied. It has been found that mixing of the organic-inorganic phases at the atomic-molecular level leads to (nano)structures that show a variety of structural arrangements. Their concrete compositions and forms strictly depend on the process of their synthesis, i.e., on the parameters of the deposition kinetics (deposition rates of fullerenes and metals, temperatures of the substrates during deposition, thickness of the deposited layers, etc.), and also on a type and (crystalline) quality of the selected substrates. When fullerenes and metals exhibit a mutual immiscibility, the final product (a hybrid film of two immiscible phases, forcibly co-existing together) is stressed and its integrity is unstable. Using energetic (ion or laser) beams and/or thermal processing, a phase separation can be triggered. It has been found that the separation might be ‘controlled’ by energy of the beam (and its fluence), or temperature and time of the annealing. It has also been proven that the phase separation can (under certain circumstances) lead to a spontaneous self-organization of the hybrid composite morphology.