The purpose of this study was to determine the dimensional accuracy of the linear and angular craniofacial measurements obtained from three dimensional computed tomography (3D CT) images using Mimics V17.0 and InVesalius 3.0 software programs. CT images were taken from archive of Hospital University Sains Malaysia (HUSM) for ten Malaysian patients. The resultant two dimensional (2D) images were stored in Digital Imaging and Communications in Medicine (DICOM) format. The segmentation of the images was prepared in Mimics V17.0 and InVesalius 3.0 softwares. Linear and angular measurements were based on craniometric anatomical landmarks pre-defined by the authors and were identified by radiologist. Ten linear and three angular measurements were repeatedly made between identified landmarks on each of the selected ten patients. Each of the linear and angular measurements was repeated 3 times and the average was taken to determine the absolute difference and percent difference between Mimics V17.0 and InVesalius 3.0 softwares. The results demonstrated no statistically significant difference in all linear and angular measurements (P>0.05) performed by two different imaging software programs and obtained from 3D CT images. Mimics and InVesalius craniofacial measurements have the same values.