Optical and structural properties of Si nanocrystals (Si-nc) in silica films are described. For the SiOx (x < 2) films annealed above 1000 °C, the Raman signal of Si-nc and the absorption coefficient are proportional to the amount of elemental Si detected by X-ray photoelectron spectroscopy. A good agreement is found between the measured refractive index and the value estimated by using the effective-medium approximation. The extinction coefficient of elemental Si is found to be between the values of crystalline and amorphous Si. Thermal annealing increases the degree of Si crystallization; however, the crystallization and the Si–SiO2 phase separation are not complete after annealing at 1200 °C. The 1.5-eV PL quantum yield increases as the amount of elemental Si decreases; thus, this PL is probably not directly from Si-nc responsible for absorption and detected by Raman spectroscopy. Continuous-wave laser light can produce very high temperatures in the free-standing films, which changes their structural and optical properties. For relatively large laser spots, the center of the laser-annealed area is very transparent and consists of amorphous SiO2. Large Si-nc (up to ~300 nm in diameter) are observed in the ring around the central region. These Si-nc lead to high absorption and they are typically under compressive stress, which is connected with their formation from the liquid phase. By using strongly focused laser beams, the structural changes in the free-standing films can be made in submicron areas.