After sustaining an injury, severed axons in the spinal cord fail to regenerate. Failure of axonal growth is related to the formation of cystic cavities within the injury site. Unlike healthy extra-cellular matrix, the cavities do not serve as permissive substrates onto which axons can attach and grow. In the current study, we developed an implantable scaffold that mimics the spinal extra-cellular matrix to encourage axonal regeneration. The scaffold was fabricated by 3D printing and freeze-drying to generate a guidance microtopography. By reconstructing an MRI scan of the lesion site, we were able to customize the scaffold’s shape to match the injury site. The scaffolds maintained their structure over four weeks in vivo and supported in vitro growth of stem cells. Hence, 3D printing can be utilized to fabricate scaffolds that are designed particularly for spinal cord injury.