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 article proposes a novel hierarchical physical design flow enabling the building of high-density and commercial-quality two-tier face-to-face-bonded hierarchical 3-D ICs. Complemented with an automated floorplanning solution, the flow allows for system-level physical and architectural exploration of 3-D designs. As a result, we significantly reduce the associated manufacturing cost compared to existing 3-D implementation flows and, for the first time, achieve cost competitiveness against the 2-D 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 $\times $ compared with 2-D, where all metrics are improved simultaneously, including up to $\mathrm {20 \%}$ power savings.