In this article, we introduce a novel method that can generate a sequence of physical transformations between 3D models with different shape and topology. Feasible transformations are realized on a chain structure with connected components that are 3D printed. Collision-free motions are computed to transform between different configurations of the 3D printed chain structure. To realize the transformation between different 3D models, we first voxelize these input models into a similar number of voxels. The challenging part of our approach is to generate a simple path—as a chain configuration to connect most voxels. A layer-based algorithm is developed with theoretical guarantee of the existence and the path length. We find that collision-free motion sequence can always be generated when using a straight line as the intermediate configuration of transformation. The effectiveness of our method is demonstrated by both the simulation and the experimental tests taken on 3D printed chains.