In current reconfigurable architectures, the interconnect structures increasingly contribute to the delay and power consumption budget. The demand for increased clock frequencies and logic availability (smaller area foot print) makes the problem even more important, leading among others to rapid elevation in power density. Three-dimensional (3D) architectures are able to alleviate this problem by accommodating a number of functional layers, each of which might be fabricated in different technology. Since power consumption is a critical challenge for implementing applications onto reconfigurable hardware, a novel temperature-aware placement and routing (P&R) algorithm targeting 3D FPGAs, is introduced. The proposed algorithm achieves to redistribute the switched capacitance over identical hardware resources in a rather "balanced" profile, reducing among others the number of hotspot regions, the maximal values of power sources at hotspots, as well as the percentage of device area that consumes high power. For evaluation purposes, the proposed approach is realized as a new CAD tool, named 3DPRO (3D-Placement-and-Routing-Optimization), which is part of the complete framework, named 3D MEANDER. Comparing to alternative solutions, the proposed one reduces the percentage of silicon area that operates under high power by 63%, while it leads to energy savings (about 9%), with an almost negligible penalty in application's delay ranging from 1% up to 5%.