$SiO_xF_y$ optical thin films of lower refractive indices than glass substrates were fabricated by the CF$_4$ ion beam assisted deposition method and the optical, structural and chemical properties of them were investigated. Refractive index of $SiO_xF_y$ films was varied from 1.455 to 1.394 by decreasing the anode voltage or from 1.462 to 1.430 by increasing the current density of end-Hall ion source. FT-IR and XPS analyses show that as the F concentration increases, the Si-O bond at $1080m^{-1}$ shifts to higher wavenumber, the OH bonds are reduced drastically, and the fluorine atoms at the air-film interface are desorbed out by reacting with $H_2O$ in the atmosphere. $SiO_xF_y$ thin films are amorphous by the XRD analysis and have the compressive stress below 0.3 GPa. As an application of $SiO_xF_y$ thin films a two-layer antireflection coating was fabricated using a $SiO_xF_y$ film as a low refractive index layer and a Si film as an absorbing one.