This paper proposes a leader following formation tracking controller for multiple underactuated underwater vehicles (UUVs) which move in three dimensional space. In order to avoid the derivative of the virtual control signals, a control method based on filter backstepping is proposed. The method can significantly simplify the design process of the backstepping controller through the use of a filter rather than the analytic derivation directly to the virtual control variable. Furthermore, the influence of measurement noise is obviously weakened. The stability of the formation system of multiple UUVs has been proved based on Lyapunov stability theory. Simulation results illustrate that the designed controller can track a three-dimensional formation trajectory accurately.