We have been using single particle electron microscopy as the major tool to study the mechanism of yeast exosome complex for RNA degradation and processing. Our most recent single particle reconstruction of yeast exosome in complex with different RNA substrates revealed two major conformations that represent different RNA recruitment pathways in the complex. A new pathway in the structure that was uncovered for the first time by our single particle EM analysis implicates a mechanism of the yeast exosome in recognizing and processing RNA substrates in specific dependence of RNA substrate’s property.