The preparation and characterization of an atomically flat and well-ordered surface on the Si(001) substrate with a buried metal layer (BML) are reported. The BML substrate was formed by implantation of Co+ ion and subsequent annealing. After molecular beam epitaxy growth of the Si overlayer on the cleaned BML sample in ultrahigh vacuum, clear 2x1 patterned and ordered steps with regular terrace width were observed by reflection high energy electron diffraction and atomic force microscopy. No contamination, including Co, was observed in the spectra of Auger electron spectroscopy and x-ray photoelectron spectroscopy. Ultraviolet photoelectron spectra showed a distinct surface peak that originated from surface dangling bonds and is characteristic of a clean and ordered surface. The surface atomic structure, including stress and damage caused by ion implantation, was characterized by medium energy ion scattering (MEIS). Very low chi(min) (1.7% with 300 keV H+) and a dip pattern in blocking profile in the MEIS spectra indicate that surface crystal quality is comparable to that of a homoepitaxially grown Si layer on normal Si substrate without BML. These results show that the BML substrate obtained by the procedure is quite useful for the structural investigation of surface species on Si by infrared (IR) reflection spectroscopy. Typical examples of IR spectra qualifying the BML substrate for surface studies are also presented.