When measuring step samples by using microscope, a wealth of step information of threedimensional shape itself is highly vulnerable to be interfered by highfrequency noise. How to maintain the step characteristics of threedimensional shape while filtering noise and achieve highprecision measurement of threedimensional shape of the sample surface information is an important research question. We did the research on wavelet denoising method based on modulus square threshold method for step threedimensional shape information by using good spacedomain and frequencydomain localization properties of wavelet function. Haar wavelet was selected for the step characteristics of the sample. The method was applied in the threedimensional height profile which was obtained through laser differential confocal microscope developed by our research group. The height measurement result of the sample after denoising is consistent with the scanning result of OLYMPUS confocal microscope. The deviation is 0.146 8 nm. It can satisfy the requirement of the followup measurement analysis of threedimensional shape information and prove the effectiveness of the algorithm.