This paper presents a design methodology for the thermal design and packaging of hybrid electronic-mechanical products. In this work, tight integration between ECAD and MCAD was achieved through the use of a web-based tool used in managing the concurrent designs, called the Domain Unified CAD Environment (DUCADE). This work also reduced the amount of time required for thermal simulation by using a web-based Design of Experiment Testbed (DOET) to systematically determine effects of varying system parameters before full-scale computational fluid dynamics (CFD) thermal modeling was performed. The design process began by proper selection of material, manufacturing process and cooling methods, based on electrical and integrated circuit design. DUCADE was then set up to monitor couplings between the various domains. This was followed by computer-aided-design and computer-aided-engineering of the mechanical package. In computer-aided-engineering, DOET was first used to determine variables that had significant effect on the thermal system response. Detailed CFD thermal simulations were then carried out in FLOTHERM only focusing on variables that the DOET determined to have strong effect. Rapid prototypes were fabricated to refine the design before final production. Each step of the cycle was tested and demonstrated through a case study on the design of the Berkeley Emulation Engine (BEE) which involved multi-disciplinary electrical, mechanical, and thermal design.