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Thermal management is one of the critical challenges in 3D integrated circuits. Incorporating thermal optimizations during the circuit design stages requires a convenient automatic method of doing thermal characterization for feedback purposes. In this paper, we present a methodology, which supports thermal characterization by automatically extracting the steady-state thermal modeling resistance network from a post-placement physical design. The method follows a two-level hierarchical approach. It does fine- grained thermal modeling for standard cells, and then at higher level assembles the thermal modeling network of the input physical design by using the built standard cell thermal models, and adding the information on inter-cell connections as well as implemented thermal management features. The methodology has been implemented in Skybridge-3D-CMOS technology, but can be employed in other fine-grained 3D directions such as monolithic 3D CMOS. Large scale benchmarking has been performed, showing the ability of doing automated fine-grained thermal characterization in the order of seconds per thousands of 3D standard cells. In addition, the methodology is employed to highlight implications of added thermal extraction features.