With the development of femtosecond laser technology and wide applications of polymethyl methacrylate (PMMA), the research on optical properties of PMMA has become a hot spot. Filamentation phenomenon appears in the process of transparent materials by femtosecond laser. Generation principles of self-focusing and filamentous are analyzed. One of the most important characteristics of laser beam is polarization state. Linearly polarized light, circularly polarized light, radially polarized light and angularly polarized light can be controlled by the combination of spatial light modulator, 1/2 wave plate and 1/4 wave plate. Generated polarized light with energy of 1 μJ is used in the line processing on PMMA, and then the comparative analysis is conduct on the length and initial position of filamentation under different polarized light. Experimental results show that linearly polarized light and circularly polarized light result in filamentation with short length, and filamentation position of linearly polarized light is close to the incident plane. Radially polarized light and azimuthally polarized light result in long length, and the distance of filamentation position to the incident plane is long.