Tight control over the amount of mRNA through formative and degradative mechanisms is important in regulating many essential cellular processes. Although much focus has been placed on transcriptional regulation, post-transcriptional forms of control such as RNA decay are receiving increasing attention. Recently, evidence suggests that in Saccharomyces cerevisiae, certain mRNAs are degraded by a novel route of decay involving autophagic targeting to the vacuole. During the post-diauxic phase, a stage of yeast growth associated with a shift from fermentation to respiration and extensive metabolic changes, apparent alterations in RNA decay and autophagy rates are observed. Specifically, some cytoplasmic RNAs may be subject to targeted autophagic transport to the vacuole, where they may undergo decay by the sole vacuolar ribonuclease Rny1. Our research examines if Rny1 clears persistent molecules called RNA decay fragments that are produced by incomplete cytoplasmic degradation of full-length mRNAs. These persistent decay fragments appear to resist other forms of RNA degradation, such as that mediated by Xrn1, suggesting a previously under-appreciated alternative route of clearance. Using an optimized northern blot procedure, the steady-state levels of these RNA species were monitored in yeast strains with and without Xrn1 or Rny1 activity. Results suggest that active Rny1 is required to effectively clear decay fragments produced from the MS2 array, a well-characterized sequence that can resist cytoplasmic decay. Xrn1 dependence for the formation of MS2 decay fragments was also observed, supporting the hypothesized route of decay fragment production. Similar conclusions were found for decay fragments originating from endogenous transcripts, such as those produced from the heat shock protein 30 (hsp30) gene. In both cases, the lack of Rny1 activity appears to cause the accumulation of decay fragments, suggesting that Rny1 is involved in the degradation of persistent byproducts of incomplete cytoplasmic RNA decay. The apparent Rny1-dependent clearance of these MS2 and genomic RNA decay fragments encourages the investigation of additional types of RNA and the elucidation of potential connections to gene regulation and pathology in other eukaryotes. Examining alternative routes of RNA decay that rely on the highly conserved process of autophagy could ultimately allow for an understanding of dysregulated RNA dynamics and neurodegenerative conditions in mammals.