Morphology changes of thin CoSi2 films close to the agglomeration threshold have been investigated by in situ scanning tunneling microscopy. Films prior to agglomeration reveal a strong morphology anisotropy where depending on direction the roughness correlation g(r) changes from logarithmic [g(r)similar to ln r] to power law [g(r)similar tor(2c) with c approximate to0.78] at short lateral length scales (r less than or equal to 30 nm). Such an anisotropy reflects the complex nature of diffusion process associated with the original anisotropic substrate surface and the formation of pinhole networks. Annealing above the agglomeration threshold (>600 degreesC), the pinhole network becomes connected breaking the CoSi2 film into aggregates with a two-dimensional fractal dimension D approximate to1.66 which is close to predictions of diffusion limited aggregation within the mean field theory prediction D=(d(2) + 1)/(d + 1) for d = 2, and invasion percolation models.