Several nanoscale devices now represent viable options to replace conventional complementary metal–oxide–semiconductor (CMOS)-based designs. The problem of logic synthesis using a nanoscale two-dimensional (2D) crossbar-switch architecture is studied herein. Despite offering several advantages, these tiny devices suffer from a high defect density because of process variations, which affects their usable area. Typically, many defective junctions appear spatially clustered in nano-crossbar structures following manufacture. Furthermore, junctions that lie in close proximity to defective ones are also prone to become faulty soon thereafter. Thus, albeit defect free, these junctions may not be reliable from the viewpoint of logic synthesis. The maximal rectangular regions in the crossbar that are devoid of any defects are identified herein. Such fault-free regions can be reliably used for mapping Boolean functions. To locate such regions, an efficient search technique based on the defect geometry is used; experimental results obtained with different crossbar sizes and defect densities are also reported. It is observed that the proposed technique outperforms earlier approaches for crossbars with clustered defects.