Purpose: The aim of this study was to evaluate the influence of voxel size and different post-processing algorithms on the analysis of dental materials using micro-computed tomography (micro-CT). Materials and Methods: Root-end cavities were prepared in extracted maxillary premolars, filled with mineral trioxide aggregate (MTA), Biodentine, and Intermediate Restorative Material (IRM), and scanned using micro-CT. The volume and porosity of materials were evaluated and compared using voxel sizes of 5, 10, and 20 µm, as well as different software tools (post-processing algorithms). The CTAn or MeVisLab/Materialise 3-matic software package was used to perform volume and morphological analyses, and the CTAn or MeVisLab/Amira software was used to evaluate porosity. Data were analyzed using 1-way ANOVA and the Tukey test (p<0.05). Results: Using MeVisLab/Materialise 3-matic, a consistent tendency was observed for volume to increase at larger voxel sizes. CTAn showed higher volumes for MTA and IRM at 20 µm. Using CTAn, porosity values decreased as voxel size increased, with statistically significant differences for all materials. MeVisLab/Amira showed a difference for MTA and IRM at 5 µm, and for Biodentine at 20 µm. Significant differences in volume and porosity were observed in all software packages for Biodentine across all voxel sizes. Conclusion Some differences in volume and porosity were found according to voxel size, image-processing software, and the radiopacity of the material. Consistent protocols are needed for research evaluating dental materials.