In thermal microscopy, temperature error arises whenever a constant emissivity value is assumed for different materials. In this paper, we propose a new approach to eliminate these undesirable effects resulting from the ambiguous surface emissivity of materials. This method enables the compensated (true) temperature distribution of a device under test to be obtained from the measured temperature image. A transfer function that relates the measured and true temperature is formed to estimate the actual temperature distribution of a biased device to an accuracy of approximately 0.3-0.7K.