“Replacement of Neanderthals by Modern Humans” (RNMH) is a project aimed at investigating possible cognitive and behavioural differences between these two human groups. I belong to the team coordinated by Naomichi Ogihara at the Keio University, and we have now published a review article about digital reconstruction of fossil crania and analysis of their brain morphology. As engineers, we are trying to reconstruct the brain anatomy of Neanderthals and early modern humans according to numerical approaches and mathematical models. Soft tissues do not fossilize, so we are trying to provide a spatial estimation of the brain anatomical organization. As a first step, restoration of the original cranial morphology is necessary, because fossil remains are often fractured, fragmented, and deformed because of the taphonomic and diagenetic processes. Digital tools and virtual simulation procedures are used to achieve a more precise and objective morphological reconstruction. Mathematical approaches are applied in such computational techniques. For example, cranial fragments are assembled based on smoothness (minimizing fitting error) of their joints. The deformation is corrected by affine transformation or thin-plate spline (TPS) function based on bilateral symmetry. Missing parts are interpolated by several mathematical approaches. This new paper reviews the current status of methods in computed anatomy, and it presents an overview on digital reconstruction of fossil crania, aimed at supplying computed methods to estimate their brain morphology.