This work presents a systematic method for the dynamic modeling of flexible multiple links that are confined within a closed environment. The behavior of such a system can be completely formulated by two different mathematical models. Highly coupled differential equations are employed to model the confined multilink system when it has no impact with the surrounding walls; and algebraic equations are exploited whenever this open kinematic chain system collides with the confining surfaces. Here, to avoid using the 4 × 4 transformation matrices, which suffers from high computational complexities for deriving the governing equations of flexible multiple links, 3 × 3 rotational matrices based on the recursive Gibbs-Appell formulation has been utilized. In fact, the main aspect of this paper is the automatic approach, which is used to switch from the differential equations to the algebraic equations when this multilink chain collides with the surrounding walls. In this study, the flexible links are modeled according to the Euler–Bernoulli beam theory (EBBT) and the assumed mode method. Moreover, in deriving the motion equations, the manipulators are not limited to have only planar motions. In fact, for systematic modeling of the motion of a multiflexible-link system in 3D space, two imaginary links are added to the real links of a manipulator in order to model the spatial rotations of the system. Finally, two case studies are simulated to demonstrate the correctness of the proposed approach.