Surface contamination of surface-enhanced Raman (SERS)-active metallic substrates has been a limitation to the utility of SERS as an analytical technique, potentially affecting surface coverage, spectral reproducibility, and analytical limits of detection. We have developed a simple and versatile cleaning method for SERS-active Ag nanorod arrays that consists of a short (4 min) exposure of the substrate to an Ar+ plasma in a low-pressure environment. The findings presented here demonstrate that this cleaning procedure essentially eliminates organic background contamination. This procedure works equally well for self-assembled monolayers of thiolates that strongly adsorb onto Au and Ag surfaces. For SERS-active surfaces composed of arrays of Ag nanorods prepared by oblique-angle vapor deposition, we investigated the (1) Raman band intensities, (2) nanorod morphology via scanning electron microscopy, and (3) surface hydrophobicity via static contact angle measurements, as a function of exposure time of the Ag nanorods to the Ar + plasma. Short (4 min) exposure to Ar+ plasma eliminated background contamination but decreased the observed SERS intensity for re-adsorbed analytes by approximately a factor of 2 while leaving the nanorod morphology essentially unchanged. Prolonged exposure to Ar+ plasma (>10 min) resulted in substantial morphological changes of the Ag nanorod lattice and led to a decrease in the observed SERS intensities by a factor of 10. The results presented here suggest that Ar+ plasma cleaning is an efficient process for removing carbonaceous and organic contamination as well as thiolate monolayers from SERS-active Ag surfaces, as long as the plasma conditions and exposure times are carefully monitored. © 2011 Society for Applied Spectroscopy.