We discuss jet substructure in recombination algorithms for QCD jets and single jets from heavy particle decays. We demonstrate that the jet algorithm can introduce significant systematic effects into the substructure. By characterizing these systematic effects and the substructure from QCD, splash-in, and heavy particle decays, we identify a technique, pruning, to better identify heavy particle decays into single jets and distinguish them from QCD jets. Pruning removes protojets typical of soft, wide angle radiation, improves the mass resolution of jets reconstructing a heavy particle decay, and decreases the QCD background. We show that pruning provides significant improvements over unpruned jets in identifying top quarks and W bosons and separating them from a QCD background, and may be useful in a search for heavy particles.