As design complexity increases with 3DICs and time-to-market becomes a critical component in the automotive, wearables and IoT segments, reducing design cycle time while maintaining accuracy of analysis has become all the more important. To address this, a system level co-design approach in step with multi-physics analysis is presented. To mitigate errors due to manual exchange of data between various engineering teams spread across chip, package and board with design and analysis adding further level of exchange, a design flow incorporating simplification at the layout level is shown. The flow enables various levels of simplified models to be used, wherein data transfer between the complex 3D structures in layout to the thermal analysis tool is automated. The efficacy of the model simplification is verified through a test case showing comparable results for the simplified and full models.