3D printed scaffolds offer a promising strategy for treating spinal cord injury (SCI). Here we present an innovative biotechnological approach for free-form 3D printing of scaffolds with a biomimetic architecture at a spatial resolution of up to a micrometer, designed for implantation in treatment of SCI in Wistar rats. The fabrication of scaffolds was based on 2-photon photopolymerization of organic polymers and was scalable to lesion geometries. The scaffolds were implemented as multiple densely packed squared parallel microtunnels (50 um per side) running their entire length. These microtunnels are separated by thin walls (5-10 um), rendering the scaffolds nearly hollow while maximizing their internal surface area. This design provides an optimal substrate, spatially aligned in the rostro-caudal direction, to support axonal and vascular ingrowth. We have found that the scaffolds, implanted in the excision of the lateral half-fragment of the spinal cord at the low thoracic level demonstrated excellent integration with surrounding tissue without the formation of a significant gliofibrous scar. Myelinated axons and oligodendrocytes, as well as vessels were observed in each microtunnel of the implanted scaffolds in 12 weeks after the operation with at least 1000 axons regenerating in the scaffold throughout its whole length. The treatment significantly improved motor function and reduced spasticity in the ipsilateral paretic limb by 8th week, with recovery sustained for at least 20 weeks. Thus, 3D oriented hollow scaffolds having a large internal surface area and direct continues microtunnels, effectively reducing axonal dispersion, mimic natural structure of the recipient tissue and create conditions for enhancing spinal cord regeneration and recovery of the motor function of the paretic limb.