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The purpose of our study was to compare the accuracy of an unconventional, non-invasive and relatively inexpensive Microscribe (3D digitizer) with a standard widely used and expensive CT-Scan and/or MRI for 3D reconstruction of a human skull, which will be used for biomechanics studies. Two models of the human skull were developed (reconstructed), one using the 3D coordinates generated by the Microscribe 3D digitizing unit and another one using the CT-Scans (2D cross-sections) obtained from a GE scanner. Both models were then subjected to stress analysis using a Finite Element Analysis program. Additionally, a few image processing software - OSIRIS, SCION IMAGE, EFILM, 3D DOCTOR and OPTIMAS - were compared in order to find the best software that could function as an interface between medical and engineering software and in the same time to have a 3D reconstruction algorithm.