Microwave wireless power transfer technology attracts attention. An RF-DC conversion circuit and its conversion efficiency is as one of most important key devices for this technology, but it is difficult to design optimum because of the nonlinear characteristics of diodes. Therefore, automatic design by the method using the Genetic Algorithm method combined to the Lumped Element Finite Difference Time Domain method has been investigated. In this paper, an encoding method which expresses a circuit pattern by patches which are allowed to overlap each other is proposed, and the result of automatic design using this method is demonstrated. In this case, there is a problem that a patch unconnected with other patches remained even with this method. To eliminate unnecessary structures remaining in the design region, an extended algorithm using the novel mutation based on fourier coefficients of current distributions on unit patches have also been proposed. Then, analysis results by this method are shown, which shows that effectively unnecessary patches can be eliminated.