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Nacre’s brick and mortar structure has been motivating innovations in biomimetic materials for decades. However, there is still room to improve understanding of the structure of the organic layer in order to engineer better biomimetic composites. A plasma-etching technique that allows for the selective removal of some organic components from individual layers is developed. We conclude that this technique enables a closer examination of the organic layer such that the locations and mechanical properties of individual components can be determined. A methodology for examining nacre samples that have not been demineralized provides a more accurate substrate for understanding the structure-property relationships of the organic layer in native nacre.