We describe the physical design and exploration methodology to optimize 3-dimensional (3D) heterogeneous Tree-based FPGA (HT-FPGA) by introducing a break-point at a particular tree level interconnect to optimize the speed, power consumption and area. The ability of the flow to decide a horizontal or vertical partitioning of the multilevel programmable tree network based on design specifications is a defining feature. The break-point of vertically partitioned tree is designed to balance the placement of logic blocks and switch blocks into multiple tiers while the break-point of horizontally partitioned tree is designed to optimize the interconnect delay of the programmable tree network. We finally evaluate the performance, area and power consumption of the proposed 3D HT-FPGA using the newly developed flow and show that vertical and horizontally partitioned 3D stacked HT-FPGA improves speed by 16% and 55% respectively. Silicon footprint reduced by 50% for vertical and 46 % for horizontal partitioning method and power consumption reduced by 35% compared to 2D counterpart.