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Abstract The embedded finite element technique provides a unique approach for modeling of fiber-reinforced composites. Meshing fibers as distinct bundles represented by truss elements embedded in a matrix material mesh allows for the assignment of more specific material properties for each component rather than homogenization of all of the properties. However, the implementations of the embedded element technique available in commercial software do not replace the material of the matrix elements with the material of the embedded elements. This causes a redundancy in the volume calculation of the overlapping meshes leading to artificially increased stiffness and mass. This paper investigates the consequences in the energy calculations of an explicit dynamic model due to this redundancy. A method for the correction of the edundancy within a finite element code is suggested which removes extra energy and is shown to be effective at correcting the energy calculations for large amounts of redundant volume.