The Multi-Material Arbitrary Lagrangian Eulerian (MMALE) method is an effective way to simulate the multi-material flow with severe surface deformation. Comparing with the traditional Arbitrary Lagrangian Eulerian (ALE) method, the MMALE method allows for multiple materials in a single cell which overcomes the difficulties in grid refinement process. In recent decades, many researches have been conducted for the Lagrangian, rezoning and surface reconstruction phases, but less attention has been paid to the multi-material remapping phase especially for the three-dimensional problems due to two complex geometric problems: the polyhedron subdivision and the polyhedron intersection. In this paper, we propose a "Clipping and Projecting" algorithm for polyhedron intersection whose basic idea comes from the commonly used method by Grandy (1999) [29] and Jia et al. (2013) [34]. Our new algorithm solves the geometric problem by an incremental modification of the topology based on segment plane intersections. A comparison with Jia et al. (2013) [34] shows our new method improves the efficiency by 55% to 65% when calculating polyhedron intersections. Moreover, the instability caused by the geometric degeneracy can be thoroughly avoided because the geometry integrity is preserved in the new algorithm. We also focus on the polyhedron subdivision process and describe an algorithm which could automatically and precisely tackle the various situations including convex, non-convex and multiple subdivisions. Numerical studies indicate that by using our polyhedron subdivision and intersection algorithm, the volume conversation of the remapping phase can be exactly preserved in the MMALE simulation. (C) 2017 Elsevier Inc. All rights reserved.