The scanning system which uses the non-linear focusing lens is usually accompanied by a major problem that is a non-constant scanning velocity of the spots in the projection plane. Moreover, the energy of the spots and the shape of the drilling holes would be affected. Hence, the focal lens of the scanning system usually uses the f-theta lens to solve this problem. This paper proposes a method utilizing the ZEMAX to analyze the commercial F-theta lens. The results indicate the F-theta lens can increase the quality of the drilling holes and amend the projection plane. In order to verify the analysis results, each diameter of an array holes drilled by the CO2 laser drilling machine would be measured. The experimental results can demonstrate that the percentage of the variation in the diameter of holes is close to the simulation results. Therefore, the method can effectively analyze the F-theta lens of the scanning systems.