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In this paper, a novel approach of automated multirobot nanoassembly planning is presented. This approach uses an improved self-organizing map to coordinate assembly tasks of nanorobots while generating optimized motion paths at run time with a modified shunting neural network. It is capable of synchronizing multiple nanorobots working simultaneously and efficiently on the assembly of swarms of objects in the presence of obstacles and environmental uncertainty. Operation of the presented approach is demonstrated with experiments at the end of the paper.