In actual joints, clearance, friction and impact forces will play an important role and can have a significant effect on the dynamic response of multibody system. In this study, the kinematic and dynamic force variables are considered in running molecular dynamics simulations, finite element simulations and macroscale system motion. To support the molecular dynamics results, finite element simulations and multibody dynamics simulations are also used to help to elucidate the size scale effects on the kinematics and dynamics between bodies. As an example, a two-linkage system was considered. A comprehensive approach to the modeling of joints with clearance in multibody systems has been presented. The problem was formulated within the framework of multibody dynamics, the finite element method and molecular dynamics approach. The impact of the rough surfaces and microscopic level contact is at least as important as the effect of joint clearance. Considering the effect of the rough surface contact and microscopic level contact in the systems dramatically increases the computational cost, and generates large amounts of "numerical noise". Time step size is an important part of the computational strategy. In the presence of clearance, the effects of dynamic behavior of microscopic level contact were found to be rather small in the sense that they had little impact on the overall dynamic response of the system if the number of microscopic contact peaks is not enough to describe the real surface of the contact areas in the macroscopic level.