Using the terms of dynamic reconfiguration and simplified fault table we have introduced an application independent fault tolerance system flow for these architectures. This flow models the architecture as a matrix and defining the problem of fault tolerance as the optimal problem of finding the biggest fault free sets applies a heuristic simulated annealing to this matrix to find some big sets of semi fault free places. Using these sets, in the final mapping exact fault detection is done using the model of bipartite graph for each set. The first step of applying simulated annealing is to find a suitable cost function. The cost function has introduced using the terms coverage and finding bigger free fault sets in the other side. By using simulated annealing defect tolerance system can prevail on the high dense of blocks in the architecture. On the other hand post reconfiguration makes the design needless of creating a huge fault map of defects places.