This paper presents utilization of argon plasma for gradual etching of calcium carbonate crystals. The plasma treatment has been chosen as it appears to be the technique that enables removal of following material layers, thus, the access to the inside of crystals is possible. Examples of investigations of the morphology and mechanical properties of surfaces of calcium carbonate crystals are presented. The impact of plasma treatment has been verified in terms of roughness and volume changes investigated using atomic force microscopy technique in a multi-step experiment. Therefore, we were able to observe the crystal degradation process, revealing the spatial inhomogeneity of the calcium carbonate crystals resulting from their core-shell structure.