A substrate processing system and a computer-readable storage medium for directing operation of a substrate processing system are provided for preparing a substrate for processing. The substrate processing system has a chamber with a substrate receiving portion and systems equipped to implement plasma processes. The computer-readable storage medium has a program that directs operation of the systems. The substrate is positioned within the chamber in a location not on the substrate receiving portion. A gaseous flow is provided to the chamber, from which a plasma is struck to heat the substrate. After the substrate has been heated, it is moved to the substrate receiving portion for processing.