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As thermal problems become more evident, new physical design paradigms and tools are needed to alleviate them. Incorporating thermal vias into integrated circuits (ICs) is a promising way of mitigating thermal issues by lowering the effective-thermal resistance of the chip. However, thermal vias take up valuable routing space, and therefore, algorithms are needed to minimize their usage while placing them in areas where they would make the greatest impact. With the developing technology of three-dimensional integrated circuits (3-D ICs), thermal problems are expected to be more prominent, and thermal vias can have a larger impact on them than in traditional two-dimensional integrated circuits (2-D ICs). In this paper, thermal vias are assigned to specific areas of a 3-D IC and used to adjust their effective-thermal conductivities. The method, which uses finite-element analysis (FEA) to calculate temperatures quickly during each iteration, makes iterative adjustments to these thermal conductivities in order to achieve a desired thermal objective and is general enough to handle a number of different thermal objectives such as achieving a desired maximum operating temperature. With this method, 49% fewer thermal vias are needed to obtain a 47% reduction in the maximum temperatures, and 57% fewer thermal vias are needed to obtain a 68% reduction in the maximum thermal gradients than would be needed using a uniform distribution of thermal vias to obtain these same thermal improvements. Similar results were seen for other thermal objectives, and the method efficiently achieves its thermal objective while minimizing the thermal-via utilization.