The dependences of self-assembled nanograting in fused silica on low repetition frequency femtosecond laser parameters and scanning parameters are investigated. The results show that the filling factor of nanograting for scanning path cross section depends on the writing parameters. The type II waveguide in fused silica can be written under some writing condition and shows polarization-dependent guiding properties. Similar polarization-dependent guiding properties with 100 kHz situation is proved in experiment by hexagonal structures assembled from type II traces. Ideal models of the cross-sectional refractive index profiles of type II waveguides and the hexagonal structures are constructed. Corresponding modes are simulated using the finite element analysis method. It is found that the polarization-dependent optical guiding properties of type II waveguides are due to polarization-dependent scattering of nanograting rather than form birefringence in theory and experiment.