We report here the growth of highly transparent nano-crystalline diamond films on quartz substrates by microwave plasma enhanced CVD. The effects of methane fraction in the source gas, substrate temperature and substrate pretreatment on the structural and optical properties of these films were studied. Optical transmission spectra, Raman spectra, surface profile as well as X-ray and transmission electron diffraction have been employed to characterize the resultant films. Variations in optical transmittance and in surface roughness as a function of methane fraction exhibited different trend for films grown with different substrate pretreatment. Specifically, comparison was made for two different grain sizes, 4 nm and 0.1 mu m, of the diamond powder used for substrate pretreatment. It was demonstrated that the major factor that controls the optical transmittance is the surface roughness provided that the sp(2)-bonded graphitic carbon in the film is avoided. Under optimized conditions, optical transmittance of greater than 84% beyond 700 nm has been obtained for films as thick as 1 mu m. Such high optical transparency of these films is primarily attributed to the high smoothness of their surface (average roughness of about 60-65 Angstrom) as well as the high content of sp(3) bonded carbon therein.