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In this paper, a mathematical model capable of handling a three-dimensional (3D) flexible n-degree of freedom manipulator having both revolute and prismatic joints is considered. This model is used to study the longitudinal, transversal, and torsional vibration characteristics of the robot manipulator and obtain kinematic and dynamic equations of motion. The presence of prismatic joints makes the mathematical derivation complex. In this paper, for the first time, prismatic joints as well as revolute joints have been considered in the structure of a 3D flexible n-degree of freedom manipulator. The kinematic and dynamic equations of motion representing longitudinal, transversal, and torsional vibration characteristics have been solved in parametric form with no discretization. In this investigation, in order to obtain an analytical solution of the vibrational equations, a novel approach is presented using the perturbation method. By solving the equations of motion, it is shown that mode shapes of the link with prismatic joints can be modeled as the equivalent clamped beam at each time instant. As an example, this method is applied to a three degrees of freedom robot with revolute and prismatic joints. The obtained equations are solved using the perturbation method and the results are used to simulate vibrational behavior of the manipulator.