Controlling topological defects in 3D liquid crystal phases is a crucial element in the development of novel devices, from bluephase 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.iquid crystals (LCs) are anisotropic materials with physical properties that depend sensitively on both global and local molecular alignment. In LCs, average local molecular orientations assume geometries that can be controlled by boundary conditions (1, 2) and external fields (3, 4), and the resulting mechanical and electric anisotropies of LCs provide powerful tools in controlling the propagation of light and the assembly of soft materials (5-10). A quintessential example is the blue-phase LC organized around a 3D disclination network (11, 12); as a display component, it offers rapid response time without surface alignment (13). The ability to tailor LCs with complex, topologically structured geometries will be necessary for the next generation of display technologies and beyond.Under appropriate boundary conditions, the smectic-A (SmA) LC phase develops a regular array of micrometer-scale defect structures known as focal conic domains (FCDs), which have gone from mere geometric curiosities to the focus of much attention in recent years as an enabling technological tool (14-17). The smectic layers in each FCD form concentric sections of Dupin cyclides, generalizations of tori, with two linear focal sets (centers of curvature), an ellipse and a confocal hyperbola (18). Whereas FCDs arise as the prototypical, kinetically trapped texture in bulk, a 2D lattice of axially symmetric toric FCDs (TFCDs) can be robustly produced in thin smectic films with antagonistic boundary conditions at the substrate and air interfaces. These TFCD arrays have been used to fabricate functional surfaces (19,20), to direct the self-assembly of soft micro...