This is a case of a 6-week-old male with D-TGA and multiple large ventricular septal defects who presented with oxygen desaturations into the 60s. He had initially undergone palliative pulmonary artery banding at a different institution, for concern that patch closure of his large ventricular septal defect would compromise ventricular function. We decided to undergo 3D printing and 4D modelling of his heart to delineate his ventricular septal defect anatomy in preparation for their closure and arterial switch operation. A 4D CTA showed a large perimembranous outlet ventricular septal defect and a very large “swiss cheese” muscular defect. We then segmented the heart and produced 3D models of the diastolic and systolic phases and printed 1- and 1.5x-sized 3D heart models. The 3D and 4D models were used to evaluate all ventricular septal defects from both sides of the ventricular septum to plan their closure. The systolic phase of the CTA demonstrated near obliteration of the apical muscular ventricular septal defects. The patient underwent complete surgical repair at 4 months. The posterior septal, apical, and large anterior muscular ventricular septal defects were closed by bovine pericardium. However, the large perimembranous and inlet ventricular septal defects were closed with a single patch, sparing the intervening muscle band that was thought to contain the conduction system. From the models, the most distal apical ventricular septal defects were shown to close with ventricular contraction during systole. Therefore, apical exclusion of the RV was not required. Thus, this additional information enabled an optimal surgical approach to efficiently close ventricular septal defects in need of closure without futile attempts at closing remote ventricular septal defects.