Modulus mapping using nanoDMA (Dynamic Mechanical Analysis) is a recently developed technique based on a nanoindentation instrument equipped with an AFM-like piezoscanner and dynamic force modulation system. The surface properties, storage and loss moduli are quantified based on the Hertz model for the contact mechanics of the sample-tip configuration. In this approach, the applied load, topography features, and their size may have a pronounced effect on the obtained results. In order to demonstrate that, internal interfaces of deep sea sponge (Monorhaphis chuni), which comprises alternating layers of relatively thick (4 μm in average) biosilica and thin (60 nm) organic material, were characterized using the nanoDMA modulus mapping technique. Experimental data were analyzed in tight interrelation with finite element simulations. This combination allowed us to evaluate elastic modulus of a 60 nm wide organic layers in M. chuni.