A new method for fabricating thin patterned CoSi2 layers has been studied. The silicide layers were generated by a solid phase epitaxy process, in which Co and Ti were deposited on a thin chemical oxide on Si(100) substrates. Rapid thermal annealing (RTA) of this structure leads to the formation of epitaxial CoSi2 with a capping layer on top. Two-step annealing in a forming ambient gas produces high quality epitaxial layers with a capping layer which can be easily removed by wet chemicals. A layer structure consisting of 30 nm SiO2 and 300 nm Si3N4, which is patterned using conventional optical lithography and dry etching, induces a stress field into the underlying layers near the patterning edges. This leads to a formation of separated CoSi2 layers during the silicide formation caused by the anisotropic diffusion of the atoms in the stress field. Such layers show nearly uniform gaps of approximately 100 nm in width.