  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.
