A method and apparatus for removing particles and residue that build up inside a substrate processing system during a substrate processing operation, without overetching system components, is described. One method includes the steps of: flowing an etchant gas comprising chlorine trifluoride (ClF.sub.3), diluted with an inert carrier gas, into a processing chamber after completion of the substrate processing operation. The parts of the system within the chamber with the greatest amount of build-up are preferentially heated to facilitate more extensive cleaning of those parts. Parts of the system within the chamber with less build up are protected from overetching by keeping them about 200.degree. C. cooler than the heavily-deposited parts. Heating the heavily-deposited chamber parts to a temperature of at least about 400.degree. C. allows using a lower concentration of etchant gas for the cleaning process than a lower temperature process would allow. The etchant gas reacts with both particles and residue in the chamber, reducing both particulate-related defects and deposition build-up. Another method includes blanketing lightly-deposited areas of the chamber with a nonreactive gas to displace and dilute the etchant gas from these areas for part of the cleaning process, while heavily-deposited areas are exposed to a higher concentration of the etchant gas for. a longer period of time. The blanketing gas is turned off for another part of the cleaning process so that these areas are also cleaned.