Bone tissue engineering strategies aimed at treating critical-sized craniofacial defects often utilize novel biomaterials and scaffolding. Rapid manufacturing of defect-matching geometries using 3D-printing strategies is a promising strategy to treat craniofacial bone loss to improve aesthetic and regenerative outcomes. To validate manufacturing quality, a robust, three-dimensional quality assurance pipeline is needed to provide an objective, quantitative metric of print quality if porous scaffolds are to be translated from laboratory to clinical settings. Previously published methods of assessing scaffold print quality utilized one- and two-dimensional measurements (e.g., strut widths, pore widths, and pore area) or, in some cases, the print quality of a single phantom is assumed to be representative of the quality of all subsequent prints. More robust volume correlation between anatomic shapes has been accomplished; however, it requires manual user correction in challenging cases such as porous objects like bone scaffolds. Here, we designed porous, anatomically-shaped scaffolds with homogenous or heterogenous porous structures. We 3D-printed the designs with acrylonitrile butadiene styrene (ABS) and used cone-beam computed tomography (CBCT) to obtain 3D image reconstructions. We applied the iterative closest point algorithm to superimpose the computational scaffold designs with the CBCT images to obtain a 3D volumetric overlap. In order to avoid false convergences while using an autonomous workflow for volumetric correlation, we developed an independent iterative closest point (I-ICP10) algorithm using MATLABÂŽ, which applied ten initial conditions for the spatial orientation of the CBCT images relative to the original design. Following successful correlation, scaffold quality can be quantified and visualized on a sub-voxel scale for any part of the volume.