He has completed nine seasons of archaeological fieldwork in the middle Usumacinta River Basin of Guatemala and Mexico. He has published a variety of articles pertaining to the archaeology of the western Maya Lowlands and is especially interested in the regional, diachronic, and comparative study of Maya polities. As a bioarchaeologist, he has researched diet and health at Piedras Negras, the population history of the Classic Maya Lowlands, violence at Colha, Belize, and royal mortuary rites at El Zotz, Guatemala. Scherer was a fellow at Dumbarton Oaks in 2008–2009. His research has been sponsored by the National Science Foundation, Wenner-Gren Foundation, National Geographic Society/Waitt Grants Program, and the Foundation for the Advancement of Mesoamerican Studies.