This disclosure includes technologies for deformation of 3D shapes using meta-handles. The disclosed 3D conditional generative system takes control points with biharmonic coordinates as deformation handles for a shape to train a network to learn a set of meta-handles for the shape. Further, each deformation axis of the latent space of deformation is explicitly associated with a meta-handle from a set of disentangled meta-handles, and the disentangled meta-handles factorize plausible deformations of the shape. Advantageously, an intuitive deformation of the shape may be generated by manipulating coefficients of the meta-handles, e.g., via a user interface.