It is anticipated that defect densities in bottom-up self-assembled nanotechnology are much higher than those in conventional VLSI technologies. Therefore, defect tolerance needs to be included in various steps of the design automation flow. In this paper, a new defect tolerant flow is proposed and a new yield metric, based on this flow, is defined. This metric is evaluated for various molecular crossbars with different defect densities. Test and diagnosis of molecular crossbars, as the main building blocks in this technology, are also investigated.