Abstract： A filter method based on biorthogonal wavelet transform was proposed to analyze the high definition metrology data, which can separate the surface three dimensional form error and waviness of multi-hole surfaces. The effectiveness of the proposed method was demonstrated by comparing it with Gaussian filtering based on simulated continuous surfaces and multi-hole surfaces. With the results obtained from continuous surfaces as references, the deviations of three dimensional waviness parameters SWa and SWt obtained from multi-hole surfaces are 153.7% and 58.3% for Gaussian filtering, and are 0.50% and 9.69% for biorthogonal wavelet transform. Moreover, the proposed method was applied in the three dimensional topography analysis of the top surface of the engine cylinder, which showed that the evaluation results of three dimensional topography for multi-hole surfaces without border distortions are accurate.