This paper discusses fundamental issues related to the integration of computer aided design and analysis (I-CAD-A) by introducing a new class of ideal compliant joints that account for the distributed inertia and elasticity. The absolute nodal coordinate formulation (ANCF) degrees of freedom are used in order to capture modes of deformation that cannot be captured using existing formulations. The ideal compliant joints developed can be formulated, for the most part, using linear algebraic equations, allowing for the elimination of the dependent variables at a preprocessing stage, thereby significantly reducing the problem dimension and array storage needed. Furthermore, the constraint equations are automatically satisfied at the position, velocity, and acceleration levels. When using the proposed approach to model large scale chain systems, differences in computational efficiency between the augmented formulation and the recursive methods are eliminated, and the central processing unit (CPU) times resulting from the use of the two formulations become similar regardless of the complexity of the system. The elimination of the joint constraint equations and the associated dependent variables also contribute to the solution of a fundamental singularity problem encountered in the analysis of closed loop chains and mechanisms by eliminating the need to repeatedly change the chain or mechanism independent coordinates. It is shown that the concept of the knot multiplicity used in computational geometry methods, such as B-spline and NURBS (nonuniform rational B-spline), to control the degree of continuity at the breakpoints is not suited for the formulation of many ideal compliant joints. As explained in this paper, this issue is closely related to the inability of B-spline and NURBS to model structural discontinuities. Another contribution of this paper is demonstrating that large deformation ANCF finite elements can be effective, in some multibody systems (MBS) applications, in solving small deformation problems. This is demonstrated using a heavily constrained tracked vehicle with flexible-link chains. Without using the proposed approach, modeling such a complex system with flexible links can be very challenging. The analysis presented in this paper also demonstrates that adding significant model details does not necessarily imply increasing the complexity of the MBS algorithm.