Two different Si(100) substrates, the 4°off-axis and the on-axis Si(100), were prepared. Ti thin films were deposited in an e-beam evaporation system and the amorphous layers of Ti-silicide were formed at different annealing temperatures. The Si(100) substrates before Ti film deposition were examined with AFM to verify the atomic scale roughness of the initial Si substrates. The amorphous layer was observed by HRTEM and TEM. And the chemical analysis and phase identification were examined by AES and XRD. The Si(100) substrate after HF clean shows the atomic scale microroughness such as atomic steps and pits on the Si surface. The on-axis Si(100) substrate exhibits much rougher surface morphologies than those of the off-axis Si(100). These differences of atomic scale roughnesses of Si substrates result in the difference of the thicknesses of amorphous Ti-silicide layers. The amorphous layer thicknesses on the on-axis exhibit thicker than those of the off-axis Si(100) and these differences inamorphous layer thicknesses became decreased as annealing temperatures increased. These indicate that the role of the atomic scale roughness on the amorphous layer thickness is much significant at low temperatures. In this study, the correlation between the atomic scale roughness and the amorphous layer thickness is discussed in terms of the atomic steps and pits based on the observation with using analysis tools such as AFM, TEM and HRTEM.