Advances in molecular electronics offer fresh opportunities for realizing newer devices by taking advantage of redox actions in molecular switches. In this paper, a nano scale Field Programmable Logic Array is proposed. The routing interconnects are implemented by nanowires while PLA based logic blocks are realized using molecular switches. By applying sufficient voltage, the state (ON/OFF) of molecular switches can be reversibly changed. Bistable switching action is the result of redox activity and hence the proposed structure can be reprogrammed repeatedly in contrast to antifuse based FPGAs. While the current antifuse devices are built with minimum dimensions reaching up to 10nm, the rotaxane molecular switch can be packed in a phenomenal smaller space of around 45 Angstroms. Nanowires as thin as 3nm and a length of few hundreds of nanometer has also been successfully fabricated. The use of nanowires will greatly reduce the dimension of FPGA structure, which for CMOS implementation is typically large. Further, rotaxane based FPGA is scalable unlike traditional CMOS FPGA with added benefits of reconfigurability and reduced size.