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Hierarchical very-large-scale integration (VLSI) flows are an understudied yet critical approach to achieving design closure at giga-scale complexity and gigahertz frequency targets. This paper proposes a novel hierarchical physical design flow enabling the building of high-density and commercial-quality two-tier face-to-face-bonded hierarchical 3D ICs. Complemented with an automated floorplanning solution, the flow allows for system-level physical and architectural exploration of 3D designs. As a result, we significantly reduce the associated manufacturing cost compared to existing 3D implementation flows and, for the first time, achieve cost competitiveness against the 2D reference in large modern designs. Experimental results on complex industrial and open manycore processors demonstrate in two advanced nodes that the proposed flow provides major power, performance, and area/cost (PPAC) improvements of 1.2 -2.2 × compared with 2D, where all metrics are improved simultaneously, including up to 20 % power savings.