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I think this is a great idea, and I truthfully have no idea how this would work other than the fact that the laws that apply to us right now on earth, apply to the molecular machines. You would need to somehow use tools smaller or the same size as the molicules themselves, then try to manipulate the molicules without them sticking to the surface of the tool. You probably need to use some type of robotic arm that can make miniscuel movements so you can therefore sucessfully create the molecular machines. Even then I still don't see the great advantage of molecular machines other than to help hospital paitents with extremely small mutations in a cell or somthing similar.