High-resolution laboratory-based thermal infrared spectroscopy is an up-and-coming tool in the field of geological remote sensing. Its spatial resolution allows for detailed analyses at centimeter to sub-millimeter scale. However, this increase in resolution creates challenges with sample characteristics such as grain size, surface roughness and porosity that can influence the spectral signature. This research explores the effect of rock sample surface preparation on the TIR spectral signatures. We applied three surface preparation methods (split, saw and polish) to determine how the resulting differences in surface roughness affects both the spectral shape as well as the spectral contrast. The selected samples are a pure quartz sandstone, a quartz sandstone containing a small percentage of kaolinite, and an intermediate-grained gabbro. To avoid instrument or measurement type biases we conducted measurements on three TIR instruments, resulting in directional hemispherical reflectance spectra, emissivity spectra and bi-directional reflectance images. Surface imaging and analyses were performed with scanning electron microscopy and profilometer measurements. We demonstrate that surface preparation affects the TIR spectral signatures influencing both the spectral contrast as well as the spectral shape. The results show that polished surfaces predominantly display a high spectral contrast while the sawed and split surfaces display up to 25% lower reflectance values. Furthermore, the sawed and split surfaces display spectral signature shape differences at specific wavelengths, which we link to mineral transmission features, surface orientation effects and multiple reflections in fine-grained minerals. Hence, the influence of rock surface preparation should be taken in consideration to avoid an inaccurate geological interpretation.