Methods for the engineering and preparation of intervertebral disc repair scaffolds and articulating joint repair scaffolds are disclosed. The methodology utilizes either magnetic resonance images or combined magnetic resonance and computed tomography images as a template for creating either the intervertebral scaffold or the joint repair scaffold (e.g., osteochondral scaffold) with fixation to the underlying bone. The disc scaffold design may include an outer annulus that may contain desired structures and a central nucleus pulposus region that could either contain a designed microstructure or a contained hydrogel. The osteochondral scaffold may include a bone compartment interface with a cartilage compartment. The bone compartment may interface with a cutout portion of the bone through fixation components. Different microstructure designs may be created for the bone and cartilage compartment to represent desired mechanical and mass transport properties. The scaffolds are designed with a microstructure that controls elastic and permeability property distribution within the scaffold.