In the frame of thermal management of electronic devices, finding efficient cooling solutions of the next generation equipment is a hot topic. If a new or improved solution is presented it always requires efficient characterization methods to prove the benefits compared to its predecessor. In case of microscale heatsink structures which are integral parts of modern chip or package level cooling concepts, an efficient measurement method is needed to analyse the performance of structures with different layouts and/or manufacturing technologies. This paper presents an enhanced thermal characterization method of microchannel based cooling structures, determining relevant partial thermal resistances from structure functions obtained by thermal transient testing. Our prior microscale heatsink characterization method was recently improved, accounting e.g. for possible nonlinearities of the heat transfer processes. This paper presents how we have improved our measurements setup in detail to deal with these phenomena compared to the previous setup.