The 3D mesh is an important representation of geometric data. It is widely used in computer graphics and has attracted more attention in computer vision community recently. However, in the generation of mesh data, geometric deficiencies (e.g., duplicate elements, degenerate faces, isolated vertices, self-intersection, and inner faces) are unavoidable. Geometric deficiencies may violate the topology structure of an object and affect the use of 3D meshes. In this paper, we propose an end-to-end algorithm to eliminate geometric deficiencies effectively and efficiently for 3D meshes in a specific and reasonable order. Specifically, duplicate elements can be first eliminated by assessing appear times of vertices or faces. Then, degenerate faces ...