An algorithm for automatic estimation of 3D transformations between two objects is presented in this paper. Skeletons of the 3D objects are created with a fully parallel thinning algorithm and feature point pairs (land markers) are extracted from skeletons automatically, and least squares method is applied to solve an over-determined linear system to estimate the 3D transformation. Experiments show that this method works quite well with high accuracy when the translations and rotation angles are small, even when there is some noise. The estimation process requires about 900 ms on an Intel Centrino Laptop with 512 MB memory, for a complex model with about 37,000 object points and 500 object points for its skeletons.