Optical properties and morphology of thin films with Ge and SiGe nanocrystallites are studied by using the methods of Raman scattering, multi-angle ellipsometry, and X-ray measurements. Our observations showed that low-temperature Ge epitaxy on Si(001) surface at 350 °C and at high growth rate leads to the formation of thin films consisting of Ge nanocrystallites with the porosity of about 50%. Deposition of Si adatoms on the film surface stimulates the reconstruction of the surface with nanocrystallites and results in the increase of the degree of Ge crystallinity, coalescence of adjacent nanocrystallites, and in a slight Si-Ge mixing. The change in the values of the optical constants due to silicon deposition is described by means of Bruggeman approximation. The main reasons for these changes are the film crystallization and the appearance of Si crystalline phase in the structures with Si capping layer. The prepared Ge nanocrystalline solids, as well as the films covered with Si, may be used in quantum dot solar cells due to the high absorption capacity of the films and devices working in the hopping regime.