This study presents a 3D version of multiscale approach for investigating magnetization dynamics in multiscale, hybrid micromagnetic-atomistic simulations. The present work introduces engineered discontinuities (i) a double-slit structure, which enables the study of domain wall and spin wave interference, and (ii) a tetrahedron shaped cluster of atoms with tunable anisotropy, which provides insights into how localized anisotropic perturbations influence domain wall pinning and skyrmion stability in fully three-dimensional (3D) hybrid simulations. We considered the dynamics of spin waves, domain walls, as well as 3D skyrmions, in the presence of these defects. The magnonic double-slit experiment demonstrates interference patterns analogous to electronic wave phenomena, offering potential applications in wave-based computing. Additionally, the results reveal the impact of the local anisotropy that leads to distinct transformations, including domain wall deformations, tubular and spherical structures, skyrmion annihilation, and breathing mode. The findings underscore the critical role of defect-induced anisotropic interactions in controlling domain wall motion, skyrmion topology, and spin wave propagation.