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In this paper Authors report the implementation of a Finite Element Method (FEM) in modelling the heat flow and the deformation of the main part of the bonding machine, the work undertaken in order to develop and optimize the technology for innovative waferlevel vacuum packaging process, addressed to high volume System-in-Package (SiP) production. The investigated new approach is based on two step MEMS (Micro Electro-Mechanical Systems) to ASIC (Application Specific Integrated Circuit) integration, realised by means of prototyped bonding station, the EVG540, developed by EVG Group . The design of experiment was carried out by Taguchi method. The relation between heat flow in analyzed system and bonding setups configuration (different compliant conditions), unit design (heat sinks, thermal insulation), materials properties (heat conductivity, emissivity, and coefficient of thermal expansion - CTE) and process conditions (vacuum level, heaters power supply, force load, and process duration) was identified and studied. The obtained results showed correlation to the bonding experimental process and confirmed the usability of the developed model. As a result, the process conditions (temperature, force load, setup configuration) were determined, and the overall bonding process can be optimized.