To explore the accurate physical visualization of customized biomedical parts using the paper-based color 3D printing, taking specific surgical training tools as tested samples, a visualization workflow was proposed and discussed with relative parameters. Three keynote elements of visualization workflow were analyzed by using model transformation, printing parameters controlling and entity evaluation from given digital congenital heart disease model, digital kidney model and digital pulmonary model. On the basis of Cutting-Bonding Framework (3D-CBF) strategy, kidney model was divided into two subblocks and layout during printing controlling phase, to develop specific principles for practical and economic physical visualization in modern surgical training applications. Since tested specimens were all captured from real pathological models accompanied with remarkable microscopic features, all these were processed with transformation adjustment to enhance practical feasibility of paper-based color 3D printer. Considering the experiencing service of surgical training parts, the physical qualities of printed biomedical parts were focused on tensile strength and surface color authenticity. According to final results of printed surgical models, the proposed paper-based 3D printing process workflow can implement vivid visualization of tested digital models, and further shared optimization suggestions for consistent physical visualization in biomedical field.