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This paper presents a methodology to generate transient compact thermal models (CTMs) for structures with multiple cooling surfaces. The generated CTMs are boundary condition independent (BCI). CTMs are presented by thermal RC networks. In our contribution, the thermal resistances and capacitances are variable related to the heat fluxes and their values change with the applied boundary conditions. The proposed method takes into account of the thermal behavior of electronic components containing several cooling surfaces and is able to deal with changing boundary conditions using linear control equations. Furthermore, the number of measurements or 3D thermal simulations to obtain the CTMs is reduced.