Thermal infrared spectral data from the Thermal Emission Imaging System (THEMIS) on Mars Odyssey can provide diagnostic information to characterize Martian surface compositions. Accurately isolating the atmospheric contribution from the thermal radiance of THEMIS data is essential for surface mineralogy analysis. In this work, we present improved semi-automatic and fully automated tools to simplify the traditional atmospheric correction method for THEMIS data. Both methods use the Thermal Emission Spectrometer surface emissivity data but in different ways. These two methods are applied to several locations that have been well documented in previous studies, to assess their capability of determining surface spectral features. The fully automatic method demonstrates its simplicity, viability, and robustness by which more consistent results have been generated for the same area across multiple THEMIS images and for areas with large topographic gradients. The tools developed in this work will broaden the utilization of THEMIS infrared spectral data to the wider planetary science community.