Abstract: The state of the surface layer of polished silicon substrates and the effect of surface-cleaning procedures, such as washing in an ultrasonic bath, etching, and vacuum annealing, is studied. The X-ray reflectivity technique is used to determine the root-mean-square (rms) roughness, thickness, and density of the damaged surface layer. It is shown that the substrates have a damaged surface layer 1.5 nm thick, which is most pronounced after annealing at 350°С. Based on the etching procedures and subsequent vacuum annealing, an approach is proposed for cleaning the surface from contaminants, the damaged layer, and obtaining substrates with a root-mean-square roughness of σ_z = 0.42 nm. This approach can be used, in particular, for the deposition of thin organic films.