Defect tolerance will become more important as feature sizes shrink closer to single digit nanometer dimensions. This is true whether the chips are manufactured using topdown methods (e.g., photolithography) or bottom-up methods (e.g., chemically assembled electronic nanotechnology, or CAEN). In this paper, we propose a defect tolerance methodology centered around reconfigurable devices, a scalable testing method, and dynamic place-and-route. Our methodology is particularly well suited for CAEN.