In the last few years, three-dimensional (3D) printing has been used in archaeology and cultural heritage fields for different purposes. Among the different technologies of 3D printing, e.g., stereolithography or selective laser sintering, this study focuses on the quality assessment of printed models using fused deposition modeling technology. To simulate archaeological human remains, a cranial model assumed as a gold standard has been printed from computed tomography (CT) data of a human skull. Eight 3D printed (3DP) models have been reproduced and CT scanned with the same protocol in order to quantify their congruence with the gold standard through an objective measurement method based on image analysis. Preliminary results show an increasing percentage error as the degree of model detail increases, from 1% to 15%. The experimental results are discussed and commented also from a metrological point of view.