Energy is vital for continual progress of human civilization. Accessing to low-cost, environmental friendly, renewable energy sources are keys to economic future for developing countries and around the globe. Wind energy systems are one of the most adequate option where power electronic converters are used for monitoring and conditioning the energy flow; however operating environmental conditions such as variable wind speed cause temperature fluctuations that derive degradation and failures in these systems. Therefore, proper thermal management and control are necessary to monitor their reliability and lifecycle. Besides, power capacity of these devices is being increased by new technological improvements such as multichip designs. Meanwhile, the heat path through the devices has also become more complex due to the heat coupling effect among several chips and it is not possible to be estimated by conventional methods found in literature. In this paper, a three dimensional finite element model (FEM) is implemented for accurate estimation of thermal profile of a power module. Based on the thermal characteristic obtained by the FEM, an electro thermal model was developed to predict the temperatures of each layer of the power module that cannot be measured during service. The work is essential as it solves massive heat transfer issues and it is important to provide health management of power electronics embedded in wind systems. Keywords-Insulated gate bipolar transistor (IGBT); two level converter; electro thermal model; junction temperature; 3D FEM.