We report on the thermal response of the transition metal/fullerene thin hybrid multilayers, pristine and ion-modified, i.e., Ni/C 60 /Ni and Ni/a-C/Ni (a-C amorphous carbon), both prepared on the MgO(100) monocrystalline substrate. The multilayer sequences were gradually annealed up to high temperatures and their structures were inspected using several analytical techniques. The inspection evidenced differences in the evolution of the virgin and ion-irradiated systems. In pristine (non-irradiated) composites (analyzed in the previous experiment) a significant part of the fullerene molecules out-diffused during annealing<500°C. At temperatures around (and above) 500°C fullerenes underwent (in the vicinity of Ni) massive fragmentation and conversion to a-C. Very high temperature (1000°C) annealing resulted in the fabrication of an array of micrometer-sized octagonal pits and rod-type particles emerging from the encompassing a-C+Ni mixture. Ion irradiated multilayers (analyzed in the current experiment) developed in a different way. Thermal annealing<500°C had only a minor effect on the integrity and composition of the system. Higher temperatures>500°C, however, induced a forceful phase separation. The nominal annealing at 1000°C resulted in the formation of facetted, sub-micrometer-sized (round, plate and rod-type) particles (with a Ni core and a thin a-C rind) that were spread individually (without a complex a-C+Ni matrix) on a thin a-C/MgO(100) interface. The main axes of the particles were oriented according to the crystallographic axis of the MgO(100) substrate.