Careful preoperative planning is of outmost importance - in particular when considering complex corrective surgery on congenitally malformed hearts. As an aid to such decision-making we describe a system for virtual reconstruction of patient-specific morphology from 3D-capable imaging modalities such as MRI and CT. We introduce and illustrate the concept of virtual cardiotomy as a new tool to preoperatively evaluate the feasibility of different surgical strategies by investigating the anatomical spatial relations through any number of virtual incisions. We review the technical and clinical implementation of the various components of the system, namely 3D imaging, segmentation and reconstruction, visualization, and simulation of tissue elasticity. Finally we summarize the main findings from a recent evaluation study on 42 infants and children.