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This paper presents a new methodology called Flex-CTM for Flexible Compact Thermal Modeling to build and to interface compact thermal models at different modeling levels. Each part of an electronic system is prepared to be Bou ndary Condition independent (BCI) such as to be plugged to other parts. Each part model is reduced to save memory and time consuming at the simulation stage. The resulting pluggable and reduced thermal model is called a micro-model. Therefore, a fast-to-simulate macro-model of a full microelectronic system can be obtained by assembling micro-models. The Flex-CTM is found to have numerous advantages over both current resistive models (junction-to-case and junction-to-board) and Dynamic Compact Thermal Models. The first advantage of the methodology is that multi-source and dynamic simulations of an electronic system can be performed at any design level. The second one is the control of the accuracy. The third advantage is the Boundary Condition Independence property that allows architecture exploration. Finally and the most important, micro and macro-models can be shared by teams to be reused and completed.