A design methodology is provided for creating biomaterial scaffolds optimized for in vivo function with any 3D anatomic shape. The method creates all designs using voxel based design techniques. It also provides for optimization of implant and scaffold microstructure to best match functional and biofactor delivery (including cells, genes and proteins) requirements. The voxel based design techniques readily allow combination of any scaffold or implant microstructure database with any complex 3D anatomic shape created by CT or MRI scanners. These designs can be readily converted to formats for layered manufacturing or casting.