Intervertebral disc (IVD) diseases are common and costly clinical problems. Current treatments are only being used to alleviate complaints caused by IVD diseases. Moreover, applied diagnoses and therapies are predominantly considered inadequate in many cases due to the difficulties encountered in the treatments of the complicated structure of the discs. Tissue engineering and regenerative medicine (TERM) approaches have been proposed to allow improved treatments for the degenerated IVD. The aim of this study was to present a semi-automatic 3D morphological segmentation of an IVD from the patient’s volumetric magnetic resonance imaging (MRI) dataset as the basic concept of patient-specific IVD scaffolds. An advanced image segmentation software was used to segment the IVD and reconstruct the corresponding 3D models. The IVD scaffolds were fabricated from PCL by 3D printing of the patient’s 3D IVD model with different lattice architectures. The samples were characterized by micro-computed tomography (micro-CT) to evaluate the effects of the lattice architecture on the morphological features. The present work steers us towards a patient-specific tissue engineering approach for IVD as herein demonstrated by the 3D printing of patient-specific scaffolds using the patient’s 3D IVD model obtained by semi-automatic segmentation from MRI. The authors would like to acknowledge the financial support provided by the Portuguese Foundation for Science and Technology (FCT) through the project EPIDisc (UTAP-EXPL/BBBECT/0050/2014), funded in the Framework of the “International Collaboratory for Emerging Technologies, CoLab”, UT Austin|Portugal Program; as well as the through the LA ICVS/3B’s project (POCI-01-0145-FEDER-007038). I.F. Cengiz thanks the FCT for the Ph.D. scholarship (SFRH/BD/99555/2014). J.M. Oliveira also thanks the FCT for the funds provided under the program Investigador FCT 2012 (IF/00423/2012).