In recent times, immersed methods such as the finite cell method have been increasingly employed in structural mechanics to address complex-shaped problems. However, when dealing with heterogeneous microstructures, the FCM faces several challenges. Weak discontinuities occur at the interfaces between the different materials, resulting in kinks in the displacements and jumps in the strain and stress fields. Furthermore, the morphology of such composites is often described by 3D images, such as ones derived from X-ray computed tomography. These images lead to a non-smooth geometry description and thus, singularities in the stresses arise. In order to overcome these problems, several strategies are presented in this work. To capture the weak discontinuities at the material interfaces, the FCM is combined with local enrichment. Moreover, the L$$^2$$
2
-projection is extended and applied to heterogeneous microstructures, transforming the 3D images into smooth level-set functions. All of the proposed approaches are applied to numerical examples. Finally, an application of cemented granular material is investigated using three versions of the FCM and is verified against the finite element method. The results show that the proposed methods are suitable for simulating heterogeneous materials starting from CT scans.