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Heterogeneous manycore architectures are the key to efficiently execute compute- and data-intensive applications. Through silicon via (TSV)-based 3D manycore system is a promising solution in this direction as it enables integration of disparate computing cores on a single system. However, the achievable performance of conventional through-silicon-via (TSV)-based 3D systems is ultimately bottlenecked by the horizontal wires (wires in each planar die). Moreover, current TSV 3D architectures suffer from thermal limitations. Hence, TSV-based architectures do not realize the full potential of 3D integration. Monolithic 3D (M3D) integration, a breakthrough technology to achieve - More Moore and More Than Moore - and opens up the possibility of designing cores and associated network routers using multiple layers by utilizing monolithic inter-tier vias (MIVs) and hence, reducing the effective wire length. Compared to TSV-based 3D ICs, M3D offers the true benefits of vertical dimension for system integration: the size of a MIV used in M3D is over 100x smaller than a TSV. In this work, we demonstrate how M3D-enabled vertical core and uncore elements offer significant performance and thermal improvements in manycore heterogeneous architectures compared to its TSV-based counterpart. To overcome the difficult optimization challenges due to the large design space and complex interactions among the heterogeneous components (CPU, GPU, Last Level Cache, etc.) in an M3D-based manycore chip, we leverage novel design-space exploration algorithms to trade-off different objectives. The proposed M3D-enabled heterogeneous architecture, called HeM3D, outperforms its state-of-the-art TSV-equivalent counterpart by up to 18.3% in execution time while being up to 19 degrees Celcius cooler.