The analysis and solution of many modern flexible multibody dynamic problems require formulations that are able to effectively model bodies with nonlinear materials undergoing large displacements and deformations. The absolute nodal coordinate formulation (ANCF) in connection with a continuum-based approach is one way to deal with these systems. The main objective of this work is to extend an existent approach for the modelling of slender structures within the ANCF framework with nonlinear, nearly incompressible materials using the volumetric energy penalty technique. The main part of the study is devoted to the evaluation of multi-layer beam models and simplifications in the locking suppression method based on F-bar projection. The results present significantly better agreement with the reference solution for multi-layer structures built with the standard ANCF beam element as compared with the earlier implementation.