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β-FeSi2 flat islands have been fabricated on ultra-thin oxidized Si(111) surfaces by Fe deposition on Si nanodots. The microstructure and interdiffusion behaviour of the β-FeSi2/Si(111) system at the atomic level were studied by using spherical aberration-corrected high-angle annular dark-field scanning transmission electron microscopy and energy dispersive X-ray spectroscopy. The formed β-FeSi2 flat islands had a disc shape with an average size of 30–150 nm width and 10–20 nm height, and were epitaxically grown on high-quality single-phase Si with a crystallographic relationship (110)β-FeSi2/(111)Si and [001]β-FeSi2/Si. Moreover, the heterojunction between the β-FeSi2(110) flat islands and the Si(111) substrate was an atomically and chemically abrupt interface without any irregularities. It is believed that these results are caused by the use of ultra-thin SiO2 films in our fabrication method, which is likely to be beneficial particularly for fabricating practical nanoscaled devices.