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This work presents the creation of a coupled analysis engine and experimental system capable of fully characterizing the thermal behavior of complex, 3D, active, submicron, electronic devices. First, the surface temperature field of an activated device is non-invasively measured with submicron spatial resolution. Next, the thermal conductivity of each thin-film layer composing the device is measured and a numerical model is built using these values. The measured temperature distribution map is then used as input for an ultra-fast inverse computational solution to fully characterize the thermal behavior of the complex 3D device. By bringing together measurement and computation, it becomes possible for the first time to non-invasively extract the 3D thermal behavior of nanoscale embedded features that cannot otherwise be accessed. The power of the method was demonstrated by verifying that it can extract details of interest of a representative MOSFET device.