Atrial fibrillation (AF) is the most common arrhythmia, but its mechanisms are still unclear. Commonly observed phenomena during AF are epicardial re-entrant drivers (rotors) and breakthrough waves. This study aims to elucidate AF mechanisms, including links between rotors and breakthroughs. We used 3D canine atrial models based on micro-CT reconstruction of biatrial geometry combined with region-specific electrophysiology models. Hence, the 3D model included ionic and structural heterogeneities in the entire atria, with special focus on the right atrium (RA) and pectinate muscles (PM). Results were visualized through 3D atrial membrane voltage maps (VM), 2D isochronal maps (IM), and wave maps (WM). AF episodes were initiated in the atria and were maintained by several epicardial rotors in the PV and RA. Transmural rotors were also seen to propagate through the PM and reemerge at the RA epicardium during these episodes. IM and WM revealed multiple breakthroughs at the region where the PM connect to the RA. The VM simulations, as well as electrogram-based IM and WM, showed that the complex AF patterns seen experimentally can be explained by the interactions of epicardial and transmural rotors.