Abstract This article illustrates a new method to align and merge two partially overlapping volumes each of them generated by cone beam computed tomography (CBCT). The aggregate volume covers a larger area of investigation and is determined by localizing one fixed LEGO brick in both of the primal volumes. Based on the LEGO brick an approximate registration of the volumes is determined. Afterwards we improve the transformation by minimizing the difference in overlapping space. In this paper we present a method which automates these two steps and provides an aligned volume.