Carbon nanotube reinforced composite materials are promising materials for the multiple potential applications in high-tech industry. Gaining the insight into the chemical composition of such materials at nanometer spatial resolution may provide a way for the improvement of manufacturing process. By combining infra-red spectroscopy (IR) and atomic force microscopy (AFM) it is possible to perform the chemical mapping with the spatial resolution down to 30 nm. The CNT nanocomposites were investigated by means of nanoIR2 and nanoIR3 systems. Infrared signal intensity measured in this method is influenced by the topography features of the investigated sample. Discussion of the correlations between the parameters recorded during the experiments will be presented in this contribution. Special attention will be given to data-processing work-flow with the help of open source software suites: R environment, ImageJ and Gwydion in order to ensure interpretability and reproducibility of the collected data. Particularly the problem of obtaining topography-free infrared absorbance signal is discussed and some possible solutions will be suggested.