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The influence of transition metal (TM = V,Co,Cu) type on the bulk diffusion induced structural changes in carbon:TM nanocomposite films is investigated. The TMs have been incorporated into the carbon matrix via ion beam co-sputtering, and subsequently the films have been vacuum annealed in the temperature range of 300 – 700 °C. The structure of both the dispersed metal rich and the carbon matrix phases has been determined by a combination of elastic recoil detection analysis, x-ray diffraction, transmission electron microscopy, and Raman spectroscopy. The as-grown films consist of carbidic (V and Co) and metallic (Cu) nanoparticles dispersed in the carbon matrix. Thermal annealing induces surface segregation of Co and Cu starting at ≥ 500 °C, preceded by the carbide-metal transformation of Co-carbide nanoparticles at ∼ 300 °C. No considerable morphological changes occur in C:V films. In contrast to the surface diffusion dominated regime where all the metals enhance the six-fold ring clustering of C, in the bulk diffusion controlled regime only Co acts as a catalyst for the carbon graphitization. These results are consistent with the metal-induced crystallization mechanism in the C:Co films. The results are discussed on the basis of the metal-carbide phase stability, carbon solubility in metals or their carbides, and interface species.