Impact of surface roughness on the atomic exchange between Si and Ge upon room-temperature adsorption of germane (GeH 4 ) at Si(001)-2×1 surface has been investigated by using temperature-programmed desorption (TPD) and multiple-internal-reflection Fourier-transform infrared spectroscopy (MIR-FTIR). Two different pretreatments of Si surfaces have been tested. On the normal surface, prepared simply by a 1200 °C flash anneal, considerable atomic exchange between Si and Ge was observed. On the epi-surface, prepared by a flash anneal followed by a Si-homoepitaxy, the atomic exchange was greatly suppressed. We relate this suppression with a possible reduction of the dimer vacancies that have been generated on the surface during the flash anneal. Suppression of surface roughness in atomic order is key to suppression of atomic exchange between Si and Ge during Ge/Si interface formation.