Controlling topological defects in 3D liquid crystal phases is a crucial element in the development of novel devices, from blue-phase displays to passive biochemical sensors. However, it remains challenging to realize the 3D topological conditions necessary to robustly and arbitrarily direct the formation of defects. Here, using a series of short pillar arrays as topological templates, we demonstrate the hierarchical assembly of focal conic domains (FCDs) in smectic-A liquid crystals that break the underlying symmetry of the pillar lattice, exhibit tunable eccentricity, and together develop a nontrivial yet organized array of defects. The key to our approach lies in the selection of the appropriate ratio of the size of focal domain to the dimension of pillars such that the system favors the "pinning" of FCD centers near pillar edges while avoiding the opposing effect of confinement. Our study unequivocally shows that the arrangement of FCDs is strongly influenced by the height and shape of the pillars, a feature that promotes both a variety of nontrivial self-assembled lattice types and the attraction of FCD centers to pillar edges, especially at regions of high curvature. Finally, we propose a geometric model to reconstruct the smectic layer structure in the gaps between neighboring FCDs to estimate the energetic effects of nonzero eccentricity and assess their thermodynamic stability.