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The Structure functions based evaluation of the thermal transient measurements is now a broadly accepted way for the characterization of the time dependent behavior of the heat flow path. The usual way of generating structure functions considers one main heat flow path. By using a large mathematical tool set it generates for this path the Rth-Cth map of the structure. This enables an easy detection of partial thermal resistances in the heat flow path, with which we can determine the values of e.g. interface thermal resistances, etc. The accuracy that we can obtain with this methodology, working on simulated results is in the order of 2-5%. In this paper we present a methodology that enhances the accuracy of the structure function based evaluation method in case of measured thermal transient curves. In this procedure on one hand we measure the thermal transients for the system to be characterized and on other hand we measure the "parasitic" heat flow path, that influences our measurement. From the processing of the two measurements theoretically the errorless structure function of the measured structure can be generated. In this paper we present this methodology with mathematical details, and prove it with measured results.