A method based on the determination of maximum common substructures is applied for the generation of substructures which are characteristic for a given set of molecular structures. The molecular structures are from hitlists obtained by spectral library searches; the hitlists contain those reference compounds, which have infrared spectra most similar to that from the query compound. The influences of various parameters of this method are investigated with the aim to improve the relevance of the obtained substructures for the structure of the query compound.