We successfully developed an arbitrary micro-patterning method with femtosecond pulses using a multi-level phase type diffractive optical element (DOE) and a focusing objective lens. The large chromatic dispersion effects of DOE resulting from the spectral bandwidth of femtosecond pulses can be reduced with the appropriate DOE focal length and the proper distance between the DOE and the focusing lens. The method was verified through optical and processing experiments. A partial periodic structure was formed at the designated position. Microstructures were precisely formed on the SiO2 glass surface and inside the glass by irradiating the constructed beam. The points were evenly dispersed with a separation of 5 mum.