In this talk, we investigate the possibilities and challenges to simulate morphological evolutions in filled polymers under applied flows. Various mesoscopic examples from polymers containing layered silicates, carbon nanotubes, and cellulose nanocrystals are discussed. In particular, dissipative particle dynamics (DPD) is highlighted as a promising tool to attack the existing challenges. The orientation of anisometric particles under shear flow is simulated at various flow conditions. The results are shown to be in good agreement with previous experiments. Furthermore, self-assembly of nanorods/nanotubes is manifested as a function of their length and content under thermodynamic conditions. It is examined how the introduction of surface charges by chemical modification leads to morphological alterations. Molecular dynamics (MD) is also represented as an underlying simulation strategy to provide DPD parameters. Moreover, the value of MD in atomistic simulations of filled polymers is emphasized by an example from highly-filled polypropylene with Fe2O3 microparticles. The conformations of polymer chains under confinement is discussed in terms of their bond orientation, segmental orientation, and chain size. We will discuss the most promising routes to couple MD, DPD, and finite element method (FEM)/finite volume method (FVM) methods to uncover a multiscale framework for the simulation of such filled systems. In this context, the strain-bridging algorithm is revisited using which one can setup a multiscale simulation of the formation of oriented microstructures of anisometric nanoparticles in polymers under shear deformations.