Effectively characterizing the behavior of deformable objects has wide applicability but remains challenging. We present a new rotation-invariant deformation representation and a novel reconstruction algorithm to accurately reconstruct the positions and local rotations simultaneously. Meshes can be very efficiently reconstructed from our representation by matrix predecomposition, while, at the same time, hard or soft constraints can be flexibly specified with only positions of handles needed. Our approach is thus particularly suitable for constrained deformations guided by examples, providing significant benefits over state-of-the-art methods. Based on this, we further propose novel data-driven approaches to mesh deformation and non-rigid registration of deformable objects. Both problems are formulated consistently as finding an optimized model in the shape space that satisfies boundary constraints, either specified by the user, or according to the scan. By effectively exploiting the knowledge in the shape space, our method produces realistic deformation results in real-time and produces high quality registrations from a template model to a single noisy scan captured using a low-quality depth camera, outperforming state-of-the-art methods.