Abstract: In recent years, digital holographic microscopy has attracted intensive attention for its capability of measuring complex shapes. There are two parts in digital holographic microscopy, hologram recording and digital diffractive reconstruction. Speckles are inevitable in the recorded interferometric patterns, thereby polluting the reconstructed surface topographies. Three reconstruction algorithms, i.e. Fresnel transform, Fresnel-wavelets and the proposed Fresnel-NSCT algorithms were compared. Three typical structures, rectangular, spherical and triangular surfaces were adopted for analysis. The performance of the three reconstruction algorithms on speckle removal and feature preservation was investigated comprehensively. Signal-Noise-Ratio(SNR) and Peak-Signal-Noise-Ratio(PSNR) were used as the numerical criteria. It is found that the Fresnel-NSCT algorithm has great superiority over the other two, subsequently it is promising for applications in the diffractive reconstruction of structured surfaces.