The chemical character, geometry, and architecture of chemically formed surface layers determine interactions between stationary phase, analyte, and mobile phase, and therefore the retention mechanisms (partitioning, adsorption, ion exchange, steric exclusion) of separated analytes. These interactions also depend on the structure and chemical character of the solutes and the composition of the mobile phase. High-molecular-weight fullerenes (C60 and C70) and water-soluble selenium-containing peptides (833 and 2607 Da) were used for the evaluation of laboratory-prepared octadecyl stationary phases with high and low coverage density before and after end-capping. The aim of this work was to study differences in surface coverage density and homogeneity and conformational changes of chemically bonded moieties and the influence of these parameters on the separation of mixtures of selenopeptides and fullerenes with significantly different molecular masses. A topographical model of the chemically modified stationary surface is presented.