Manipulation of nanomaterials such as nanoparticles (NPs) and nanorods (NRs) to make clusters is of significant interest in material science and nanotechnology due to the unusual collective opto-electric properties in such structures that cannot be found in the individual NPs. This work demonstrates an effective way to arrange NP clusters (NPCs) to make the desired arrays based on removable and NP-guidable liquid crystalline template using sublimation and reconstruction phenomenon. The position of the NPCs is precisely controlled by the defect structure of the liquid crystal (LC), namely toric focal conic domains (TFCDs), during thermal annealing to construct the LC and corresponding NPC structures. As a proof of concept, the surface-enhanced Raman scattering (SERS) activity of a fabricated array of gold nanorod (GNR) clusters is measured and shown to have highly sensitive detection characteristics essential for potential sensing applications.