The additively manufactured parts suffer from thermal shrinkage and deformation, leading to an unacceptable dimensional accuracy. The anisotropic and non-uniform local shrinkage and deformation make the problem very complex. This paper presents an easy-to-use and effective approach to generate a compensated geometry so that the printed part of the compensated geometry meets the dimensional tolerance. The proposed approach only requires a few measured dimensions that are critical for applications. The designed 3D model is first converted as a triangle mesh with vertices and triangle faces. Each vertex is associated with a local affine transformation, and also a global scaling transformation is applied to all vertices. By tuning the parameters of the global and local affine transformations, the triangle mesh can morph to fit with the measured dimensions. We set four physical constraints to regulate the shape morph, including smoothness, rigidness, measured dimensions and flat bottom. These constraints are formulated as a minimization problem with thousands of variables, which can be efficiently solved by Levenberg-Marquardt Algorithm within a minute. Then the compensated 3D model is generated using the reverse affine transformations for each vertex with the obtained optimal parameters. We test our method on a case study, which shows that the dimensional error is reduced by 69.7 percent on average.