We present a CAD framework for CMOL, a hybrid CMOS/ molecular circuit architecture. Our framework first transforms any logically synthesized circuit based on AND/OR/NOT gates to a NOR gate circuit, and then maps the NOR gates to CMOL. We encode the CMOL cell assignment problem as boolean conditions. The boolean constraint is satisfiable if and only if there is a way to map all the NOR gates to the CMOL cells. We further investigate various types of static defects for the CMOL architecture, and propose a reconfiguration technique that can deal with these defects through our CAD framework. This is the first automated framework for CMOL cell assignment, and the first to model several different CMOL static defects. Empirical results show that our approach is efficient and scalable.