Despite significant advances in 3D biomaterial printing, the potential of 3D printing for patient specific implants and tissue reconstruction has not been fully exploited. This is due in part to the lack of integration of image-based patient specific design with 3D biomaterial printing within a relevant regulatory framework, namely design control, required by the FDA. In this manuscript, we describe the integration of image-based, multi-scale patient specific design with 3D biomaterial printing within a design control framework for clinical translation. Specifically, we define design inputs for patient specific implants and scaffolds, and utilize image-based patient specific design to achieve these design inputs. We then illustrate realization of these topology designed patient specific implants by laser sintering of polycaprolactone (PCL). Finally, we present initial results in large animal models using 3D printed PCL implants addressing two challenging problems in tissue reconstruction: 1) designing and 3D printing implantable devices to allow growth in pediatric airway applications and 2) utilizing 3D printed scaffolds as foundations for pre-fabricated flaps to obtain vascularization and bone formation for large volume bone/soft tissue reconstruction. We illustrate these challenging problems as they need to be incorporated in design control, but as of yet there is little data to direct how growth and vascularization should be utilized in design control.