Epitaxial growth of CoSi2on (111)Si inside two‐dimensional and linear oxide openings by rapid thermal annealing has been investigated by transmission electron microscopy. Both annealing temperature and time were found to be critical in obtaining 100% epitaxy. The size of oxide openings and annealing temperature were found to exert strong influences on the morphology of epitaxial CoSi2on silicon. The faceting of CoSi2was found to occur at a lower temperature inside oxide openings of smaller size. The change in morphology of epitaxial CoSi2with the size of oxide openings in the present study indicated that interfacial energy and/or stress, in addition to the surface energy, are important in determining the morphology of epitaxial CoSi2on (111)Si.