The objective of this paper is to demonstrate the use of the Absolute Nodal Coordinate Formulation (ANCF) in the integration of Finite Element (FE) and MultiBody System (MBS) algorithms for modeling the rigid body contact and the ligament flexibility in bio-mechanics applications. To this end, a general formulation based on ANCF finite elements for modeling the contact in bio-mechanics applications is presented. Each contact surface is described in a parametric form using two surface parameters that enter into the ANCF finite element geometric description. A set of nonlinear algebraic equations that depend on the surface parameters are developed. These nonlinear algebraic equations are solved itertively in order to determine the location of the contact points. This formulation is implemented in a general MBS algorithm that allows for modeling rigid and flexible bodies. ANCF finite elements can also be used to describe the large displacement of the ligaments, muscles, and soft tissues (LMST). The computational algorithm developed in this investigation can be demonstrated using a knee joint model in which the ACL and PCL are modeled using linear spring damper elements and the LCL and MCL are modeled using the large displacement ANCF finite elements that allows for using general constitutive models and capture the deformation of the ligament cross sections.