Packaged NERS-active structures are disclosed that include a NERS substrate having a NERS-active structure thereon, and a packaging substrate over the NERS substrate having an opening therethrough, the opening in alignment with the NERS-active structure. A membrane may cover the opening in the packaging substrate. In order to perform nanoenhanced Raman spectroscopy, the membrane may be removed, and an analyte placed on the NERS substrate adjacent the NERS-active structure. The membrane may be replaced with another membrane after the analyte has been placed on the substrate. The membrane may maintain the pristine state of the substrate before it is deployed, and the replacement membrane may preserve the substrate and analyte for archival purposes. Also disclosed are methods for performing NERS with packaged NERS-active structures.