Nonrigid or deformable 3D objects are common in many application domains. Retrieval of such objects in large databases based on shape similarity is still a challenging problem. In this paper, we first analyze the advantages of functional operators, and further propose a framework to design novel shape signatures for encoding nonrigid object structures. Our approach constructs a context-aware integral kernel operator on a manifold, then applies modal analysis to map this operator into a low-frequency functional representation, called fast functional transform, and finally computes its spectrum as the shape signature. Our method is fast, isometry-invariant, discriminative, and numerically stable with respect to multiple types of perturbations.