Abstract: Using excimer laser to manufacture polymer materials can get more ideal biochips.Considering the needed performances of materials used in fabrication of biochips,PMMA and PC's properties are compared.These properties involve in the transmittance of light waves of different wavelengths.The micro-structure of polymer materials after micromachined by excimer laser,the correlation of the ablation depth per pulse with different fluences of excimer laser for different polymers is measured.The energy of KrF excimer laser can be totally absorbed by PMMA and PC,therefore micromachining of biochip can be done by using excimer laser on PMMA and PC's surfaces.The influence on detection quality of PMMA is smaller than PC.The ablation depth per pulse of PMMA to excim er laser is higher than PC under the same fluence.PMMA is manufactured more easily but the quality of micro-structure ablated is worse than PC because of different reaction mechanics to excimer laser.