Three-dimensional Electron Back Scattering Diffraction (3D-EBSD)is a technique for microstructure characterization that works by sequential sectioning via mechanical polishing, Focused Ion Beam (FIB)milling or layer ablation by laser. In this technique, consecutive steps of sample preparation and EBSD measurement are employed to extract 2D-EBSD sections and to reconstruct the 3D microstructure. The 3D data collected by the serial sectioning technique, suffer from misalignment between the adjacent sections. In the present work, serial sectioning by mechanical polishing was employed to collect 3D EBSD data of a dual-phase (DP)steel sample. A previously developed algorithm based on the minimization of misorientation between the neighboring sections was utilized to accurately align the consecutive sections. The reconstructed microstructure was then used to validate the accuracy of the alignment algorithm. The results show that the alignment procedure has successfully improved the reconstructed 3D microstructure and produced reconstructed sections, which in terms of microstructural parameters (i.e. grain size and morphology), image quality and kernel average misorientation distribution resemble the results of a directly measured EBSD experiment and can be used to differentiate the 3D morphology and crystallography of martensite from ferrite in DP steels.