In this work we set to examine several important issues pertinent to currently very active research area of the finite element modeling of flexible multibody system dynamics. To that end, we first briefly introduce three different model problems in non-linear dynamics of flexible 3D solid, a rigid body and 3D geometrically exact beam, which covers the vast majority of representative models for the particular components of a multibody system. The finite element semidiscretization for these models is presented along with the time-discretization performed by the mid-point scheme. In extending the proposed methodology to modeling of flexible multibody systems, we also present how to build a systematic representation of any kind of joint connecting two multibody components, a typical case of holonomic contraint, as a linear superposition of elementary constraints. We also indicate by a chosen model of rolling contact, an example of non-holonomic constraint, that the latter can also be included within the proposed framework. An important aspect regarding the reduction of computational cost while retaining the consistency of the model is also addressed in terms of systematic use of the rigid component hypothesis, mass lumping and the appropriate application of the explicit-implicit time-integration scheme to the problem on hand. Several numerical simulations dealing with nonlinear dynamics of flexible multibody systems undergoing large overall motion are presented to further illustrate the potential of presented methodology. Closing remarks are given to summarize the recent achievements and point out several directions for future research.