This paper presents an automated pipeline that aligns and prunes 3DGS scenes against a reference 3D mesh through a systematic six-stage process, inside a 3D reconstruction workflow. Our methodology addresses key challenges in automated 3D reconstruction including adaptive parameter selection, noise handling, geometric preservation, and quality assessment. Experimental validation on three model reconstructions demonstrates the system's effectiveness, including validation metrics from structural analysis, segmentation accuracy, surface reconstruction fidelity, and alignment precision. This integrated pipeline provides a computational foundation for automated 3D reconstruction of complex structures with photorealistic rendering and topological modeling, supporting applications in robotics, simulation & infrastructure inspection.
