Femtosecond laser at 1040 nm centre wavelength with 190 fs pulse width and variable (200~5000 kHz) repetition rate has been applied to microfabricate fused silica. Threshold energy has been measured as a function of the pulse repetition rate and the scan speed. The role of thermal diffusion and heat accumulation effects in forming waveguide is demonstrated. Double-line waveguides with the optimal parameters have been written, where the guided mode is fundamental mode and nearly circular. Hexagonal microstructure waveguide with elliptical cells has been made, where the mode has a nearly Gaussian intensity profile at 1040 nm. The microstructure waveguide has a large mode area about 247.48 μm2 and single polarization propagation property with extinction ratio about 9.05. The numerical aperture of the waveguide is about 0.017.