Controlling the organization of self-assembling building blocks over a large area is crucial for lithographic tools based on the bottom-up approach. However, the fabrication of liquid crystal (LC) defect patterns with a particular ordering still remains a challenge because of the limited close-packed morphologies of LC defects. Here, we introduce a multiple-stamping domain separation method for the control of the dimensions and organization of LC defect structures. Prepatterns with various grid shapes on planar polyimide (PI) surfaces were fabricated by pressing a line-shaped stamp into the PI surfaces in two different directions, and then these surfaces were used to prepare LC defect structures confined to these grid domains. The dimensions of the LC defect structures, namely, the equilibrium diameter and the center to center spacing, are controlled by varying the line spacing of the stamps and the film thickness. A variety of arrangements of LC defects, including square, rhombic, hexagonal, and other oblique lattices, can be obtained by simply varying the stamping angle (Omega) between the first and second stamping directions. Furthermore, we demonstrate that the resulting controllable LC defect arrays can be used as templates for generating various patterns of nanoparticles clusters by trapping quantum dots (QDs) within the cores of the LC defects.