The epitaxial growth of β-FeSi 2 films produced on flat and patterned Si(001) substrates under various substrate temperatures (T s ) with deposition rates of Fe (V Fe ) was investigated by transmission electron microscopy (TEM). In the film deposited on the flat Si(001) substrate, precipitates of flat-bottom shaped β-FeSi 2 and those of round-bottom shaped α-FeSi 2 were formed at T s =500 °C and V Fe =0.02 nm/s. The β-FeSi 2 adopted the epitaxy to (001) Si plane, while α-FeSi 2 selected the epitaxy to {111} Si planes inside the Si matrix. At T s =350 °C and V Fe =0.01 nm/s, a continuous β-FeSi 2 layer were formed epitaxially on the Si(001) substrate without forming α-FeSi 2 . It was found that the lower temperature and the higher Fe-concentration suppress the formation of α-FeSi 2 and promote the formation of β-FeSi 2 . In addition, the morphology of β-FeSi 2 changed from fine isolated precipitates (islands) to a continuous layer with increasing the deposition rate and the substrate temperature. In the film deposited on the patterned Si(001) substrate at T s =500 °C and V Fe =0.02 nm/s, on the other hand, both β- and α-FeSi 2 precipitates were formed on the top-hills and the valleys of the patterned substrate, while only α-FeSi 2 precipitates were formed on the sidewalls. These results demonstrate that not only the growth conditions but also geometric situations affect strongly the epitaxial growth of FeSi 2 precipitates.