Systems and methods for gas flow in a thermal processing system are provided. In some example implementations a gas flow pattern inside the process chamber of a millisecond anneal system can be improved by implementing one or more of the following: (1) altering the direction, size, position, shape and arrangement of the gas injection inlet nozzles, or a combination hereof; (2) use of gas channels in a wafer plane plate connecting the upper chamber with the lower chamber of a millisecond anneal system; and/or (3) decreasing the effective volume of the processing chamber using a liner plate disposed above the semiconductor substrate.