Methods of determining the endpoint of cleaning residues from the internal surfaces of a chemical vapor deposition chamber are described. The methods are especially useful for determining when organic-based residues deposited from an ultra low-k film precursor deposition are removed from the chamber. The methods involve cleaning the chamber with a plasma comprising fluorine and oxygen while monitoring the intensity of the optical emission lines of one or more atomic or molecular species that correlate to the removal of the organic-based residues. Techniques and apparatuses for monitoring different appropriate emission lines are described. Methods of the invention can be used to prevent particle contamination during CVD operations following ultra low-k film precursor depositions and improve wafer throughput in manufacturing environments.