The use of a CO2 laser system for fabrication of microfluidic chip on polymethyl methacrylate (PMMA) is presented to reduce fabrication cost and time of chip. The grooving process of the laser system and a model for the depth of microchannels are investigated. The relations between the depth of laser-cut channels and the laser beam power, velocity or the number of passes of the beam along the same channel are evaluated. In the experiments, the laser beam power varies from 0 to 50W, the laser beam scanning velocity varies from 0 to 1 000 mm/s and the passes vary in the range of 1to 10 times. Based on the principle of conservation of energy, the influence of the laser beam velocity,the laser power and the number of groove passes are examined. Considering the grooving interval energy loss, a modified mathematical model has been obtained and experimental data show good agreement with the theoretical model. This approach provides a simple way of predicting groove depths. The system provides a cost alternative of the other methods and it is especially useful on research work of microfluidic prototyping due to the short cycle time of production.