A novel fabrication method has been developed for the preparation of a periodic array of nanoparticle clusters (NPCs) using a sublimable liquid crystal (LC) material. The defect structures of the LC film provide the specific topographical confinement to trap nanoparticles (NPs) and assemble the NPs to generate NPCs during thermal annealing. This system shows a simple regulation of the size of NPCs by varying the concentration of the NP-suspension. Additionally, an illumination system using quantum dots (QDs) is fabricated using the manipulation method reported here.