The guided-mode resonance senor plays an important role as a major dissipation layer in an opt-ical waveguide. In this study, we report the fabrication and characterization of inner optical wave-guide layers based on fused-silica and PMMA plates by a femtosecond fiber laser machining system. The wavelength and repetition rate of the femtosecond fiber laser are 532 nm and 1 MHz, respec-tively. We investigated two main fabrication parameters for forming the inner waveguide, laser power and scanning speed. Results show that the modified width of inner waveguide decreases with increasing scanning speed. By analyzing the net fluence of the laser pulses in fabricating the wave-guide, the energy range for successfully formed waveguide in the fused silica and PMMA plates are found within 0.973 - 1.216 - KJ/cm2 and 0.363 - 0.635 KJ/cm2, respectively