Elastic modulus of commonly used excipient, i.e. microcrystalline cellulose (MCC) and an active pharmaceutical ingredient (API), i.e. clarithromycin has been measured by atomic force microscopy. Moderate forces applied with AFM cantilever caused small deformations (a few nanometers) of investigated samples and under such conditions the Hertz model was successfully applied. Wide distributions of the measured elastic modulus imply on heterogeneous surface properties of the investigated samples. This could be explained by polycrystalline attributes of clarithromycin and coarse structure of MCC agglomerates. AFM-based nanoindentation method was compared to a permanent indentation technique performed by nanoindenter. Results obtained by applying larger forces using nanoindenter showed a significant indentation depth dependence that could be the consequence of materialćs non-ideally elastic surface or viscoelastic/plastic properties.