1. A computer-implemented method for modifying a three-dimensional (3D) model in a shape editing system, comprising: (a) obtaining the 3D model in the shape editing system; (b) selecting one or more first faces (S) of the 3D model; (c) identifying a set of one or more second faces(S′) that are fixed, wherein the one or more first faces do not overlap with the one or more second faces; (d) prescribing shape modification operations to be performed on the one or more first faces (S); (e) constructing a deformation lattice by: (1) setting up a lattice structure with control points, wherein parametric space (u,v,w) is defined in terms of vertices of the lattice structure; (2) mapping Euclidean space (x,y,z) of the 3D model to the parametric space (u,v,w) of the lattice structure; (f) evaluating the deformation lattice by: (1A) when the shape modification operation comprises an affine transformation, applying the affine transformation directly on a selected set of the control points; (1B) when the shape modification operation does not comprise an affine transformation, deforming the deformation lattice based on a discrete fitting problem; and (g) outputting a deformed 3D model based on the evaluated deformation lattice.