A network approach to the macroscopic anatomy of the human brain can be used to model physical interactions among regions in order to study their topological properties, as well as the topological properties of the overall system. Here, a comprehensive model of human brain topology is presented, based on traditional macroanatomical divisions of the whole brain, which includes its subcortical regions. The aim was to localise anatomical elements that are essential for the geometric balance of the brain, as to identify underlying phenotypic patterns of spatial arrangement and understand how these patterns may influence brain morphology in ontogeny and phylogeny. The model revealed that the parahippocampal gyrus, the anterior lobe of the cerebellum and the ventral portion of the midbrain are subjected to major topological constraints that are likely to limit or channel their morphological evolution. The present model suggests that the brain can be divided into a superior and an inferior morphological block, linked with extrinsic topological constraints imposed by the surrounding braincase. This information should be considered duly both in ontogenetic and phylogenetic studies of primate neuroanatomy.