The finite element absolute nodal coordinate formulation (ANCF) is often used in modeling very flexible bodies in multibody system (MBS) applications. This formulation leads to a constant mass matrix, allowing for an efficient sparse matrix implementation. Nonetheless, the use of the ANCF finite elements to model stiff structures can lead to high frequencies associated with ANCF coupled deformation modes, as discussed in the literature. Implicit numerical integration methods can be effectively used to develop efficient procedures for the solution of MBS differential/algebraic equations. Most existing implicit integration algorithms, however, require numerical differentiation of the equations of motion, and some of these integration methods do not ensure that the kinematic algebraic constraint equations are satisfied at all levels (position, velocity, and acceleration). Because of these limitations, existing implicit integration methods can be less accurate and less efficient when used to solve large scale MBS applications. In order to circumvent this problem, the two-loop implicit sparse matrix numerical integration (TLISMNI) method was proposed for the solution of MBS differential/algebraic equations. The TLISMNI method does not require numerical differentiation of the forces and allows for an efficient sparse matrix implementation. This paper discusses TLISMNI implementation issues including the step size selection, the error control, and the effect of the numerical damping. The relation between the step size selection and the structure stiffness is also discussed. The use of the computer implementation described in this paper is demonstrated by solving very stiff structure problems using the Hilber–Hughes–Taylor (HHT) method, which includes numerical damping. An eigenvalue analysis and Fast Fourier Transform (FFT) are performed in order to identify the fundamental modes of deformation and demonstrate that the contributions of these fundamental modes can be erroneously damped out when some other implicit integration methods are used. The TLISMNI method, on the other hand, captures the contributions of these fundamental modes. The results, obtained using the TLISMNI method, are compared with the results obtained using other methods including the implicit HHT-I3 and the explicit Adams integration methods. The results obtained show that the TLISMNI method can be five times faster than the other two methods when no numerical damping is considered.