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3D IC technologies can help to improve circuit performance and lower power consumption by reducing wirelength. Also, 3D IC technology can be used to realize heterogeneous system-on-chip design, by integrating different modules together with less interference with each other. In this paper, we propose a novel thermal-aware 3D cell placement approach, named T3Place, based on transforming a 2D placement with good wirelength to a 3D placement, with the objectives of half-perimeter wirelength, through-the-silicon (TS) via number and temperature. T3Place is composed of two steps, transformation from a 2D placement to a 3D placement and the refinement of the resulting 3D placement. We proposed and compared several different transformation techniques, including local stacking transformation (LST), folding-2, folding-4 and window-based stacking/folding transformation, and concluded that (i) LST can generate 3D placements with the least wirelength, (ii) the folding-based transformations result in 3D placements with the fewest TS vias, and (iii) the window-based stacking/folding transformations provide good TS via number and wirelength tradeoffs. For example, with four device layers, LST can reduce the wirelength by over 2times compared to the initial 2D placement, while window-based stacking/folding can provide over 10times variation in terms of the TS via number, thus adaptive to different manufacturing ability for TS via density. Moreover, we proposed a novel relaxed conflict-net (RCN) graph-based layer assignment method to further refine the 3D placements. Compared to LST results, thermal-aware RCN graph-based layer assignment algorithm (r = 10%) can further reduce the maximum on-chip temperature by 37%, with only 6% TS via number increase and 8% wirelength increase.