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Our use of a commercially available monolithic surface enhanced Raman spectroscopy substrate based on metallized arrays of nanopillars has been hindered by the structured and variable background spectrum found in as‐supplied substrates. We identify surface contamination—at minimum from the shipping container—as the root cause of the variability and observed that our cleaning protocol could enhance the spectral performance but could also significantly degrade it in some cases. These uniquely nanostructured substrates offer on‐demand hot spot formation by solvent‐evaporation‐induced nanopillar leaning, so that oxygen‐plasma treatment was used as a noncontact method to preserve this capability. Suitable plasma cleaning conditions produced less structured background spectra and yielded higher signal intensities. Detrimental plasma power and exposure durations could yield significantly cleaner background spectra but at the significant cost of response to analyte. Scanning electron micrographs showed the plasma could alter the surface morphology. Optimization of oxygen‐plasma settings must therefore balance favorable effects such as contaminant removal, improved substrate wetting, and signal enhancement with deleterious effects such as structural damage to the substrate. [ABSTRACT FROM AUTHOR]