Machine assisted systems and methods for anisotropic polyhedral boundary layer adaptation that provides an anisotropic refinement of polyhedral prisms are described. The method can include operations: identifying a prismatic polyhedral cell as a parent cell within a polyhedral mesh representing an object of a physical system; generating a plurality of child cells for the parent cell based on non-overlapping child faces of a side face as a parent face, wherein a pair of mid-edge nodes for the side face are connected anisotropically for a child face edge of the non-overlapping child faces, the pair of mid-edge nodes are connected between the two base edges or between the two side edges; and refining the polyhedral mesh until a refinement level or a size limit is obtained, wherein the refining the polyhedral mesh includes the identification of the prismatic polyhedral cell and the generation of the plurality of child cells.