Two-dimensional (2D) photonic crystal patterns have been fabricated by an improved nanosphere lithography method. By introducing an intermediary SiO2 layer between the self-assembled layer and the substrate, this method can be applied to a wide range of materials without much concern for their surface hydrophilicity. The controllability of the photonic crystal patterns has also been investigated. The air-filling factor of the photonic crystal patterns can be easily tailored by thinning the polymer nanospheres in inductively coupled O2 plasma with a controllable etch rate. Large-area ordered 512 nm pitch hole array, with vertical and smooth sidewalls, has been successfully formed on a GaAs substrate, indicating the potential application in photonic crystal devices of this method.