We used scanning tunneling microscopy (STM) to study the Cu-induced restructuring of Si(100)-(2 × 1) surface at the atomic scale. Copper was deposited onto silicon substrates kept at room temperature (RT) or 500 °C. Submonolayer amounts of Cu were found to be sufficient to induce a visible restructuring of the Si(100)-(2 × 1) surface manifested by the disappearance of the vacancy line defects (VLDs), as well as dimer rows disordering (for the RT deposition) or the formation of a c(4 × 4) surface reconstruction (for the 500 °C deposition) not reported for the Cu/Si(100) system so far. Higher amounts of Cu deposited onto the RT-disordered surface at 500 °C led to the formation of 3D CuSi crystallites, accompanied by a significant surface roughening. In contrast, deposition of large amounts of Cu onto a pristine Si(100) at 500 °C resulted in the formation of a near-(1 × 1) local surface atoms ordering.