We present an approach for estimating the relative transformations between fragments of a broken cylindrical structure in 3d. To solve this problem, we first measure the orientation and position of the cylinder axes for each fragment by an adapted kind of Hough Transformation. The cylinder axes are an important feature for separation of fractured areas and for calculation of an initial reposition solution (constraining 4 DOFs). After these processing steps, we compute the relative transformations between corresponding fragments by using well-known surface registration techniques, like 2d depths correlation and the ICP (Iterative Closest Point) algorithm. One goal of our project is to use the proposed method for estimation of relative transformations between fragments of fractured long bones for computer aided and semi-automatic bone alignment and fracture reduction in surgery.