Background: The application of new imaging software for the reconstruction of left atrium (LA) geometry during atrial fibrillation (AF) ablation has not been well investigated. Methods: A total of 27 patients undergoing AF ablation using a CARTO Segmentation Module system were studied (phase I). High-density LA mapping using PentaRay was merged with computed tomography-based geometry from the auto-segmentation module. The spatial distortion between the two LA geometries was analyzed and compared using Registration Match View. The associated contact force on the two LA shells was prospectively validated in 16 AF patients (phase II). Results: Of the five LA regions, the roof area had the highest quality score between the two LA shells (1.7 ± 0.6). In addition, among the pulmonary veins (PVs), higher quality scores were observed in bilateral PV carinas (both 1.8 ± 0.1, p < 0.05) than in the anterior or posterior PV regions. Furthermore, surrounding the PV ostium, the on-surface points had a significantly higher contact force when targeting the high-density fast anatomical mapping shell than for the auto-segmentation module (right superior pulmonary vein, 20.7 ± 5.8 g vs 12.5 ± 4.4 g; right inferior pulmonary vein, 19.3 ± 6.8 g vs 11.8 ± 4.8 g; left superior pulmonary vein, 22.5 ± 7.3 g vs 11.2 ± 4.5 g; left inferior pulmonary vein, 15.7 ± 6.9 g vs 9.7 ± 4.4 g, p < 0.05 for each group). Conclusion: The CARTO Segmentation Module and Registration Match View provide better anatomic accuracy and less regional distortion of the LA geometry, and this can prevent excessive contact and potential procedural complications.