Human skeletal remains are analysed by forensic anthropologists in order to draw conclusions about the probable identity of the deceased. During the analysis, the skull is used, along with other bones, to help determine the identity of the decedent. If only the base of the skull is available, forensic researchers take manual measurements from the large oval aperture in this region, the foramen magnum, in order to obtain information about the gender of the deceased. As this operation requires human intervention, the measurements are affected by the bias introduced by the human operator. The aim of this paper is to describe a full machine vision solution to perform precise morphological measurements of the foramen magnum. The system has been designed to extract measurements from 2D and 3D data and the returned results accurately match the manual measurements.