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Trajectory estimation design of tactical ballistic missiles (TBM) is an important issue to build up an anti-missile system and attracts a lot of attentions in it. Unfortunately, the relative trajectory estimation technologies are still secrets of "specific countries" and of course, cannot be easily obtained. Based on this reason, in this research, an advanced trajectory estimation design is investigated with combined the input estimation and extended Kalman filter. In this proposed method, estimation abilities extend from high speed reentry target's position and velocity to uncertain maneuverable accelerations and ballistic coefficient, i.e., more information of the targets can be offered by this method, besides, the acceptable trajectory estimation performance are shown from scenarios with different testing conditions.