The shape control problem involves deforming a non-rigid object into a desired shape. In this paper, we present a new 3D shape control method that can handle large deformations of texture-less objects. In particular, we use functional maps to generate surface points' correspondences between the current and the desired shape that serve as input for our Procrustes-based multi-scale control strategy. The main contribution is a multi-scale analysis with a relaxed rigidity assumption that defines scales based on geodesic distances to the grippers. Our method considers that objects may deform at different scales depending on the gripper actions applied to them. For this reason, our multi-scale analysis computes shape control actions defined according to gripper influence on particularly convenient scales. We present stability analysis and discuss several simulations and experiments.