Embodiments of the present disclosure generally relate to methods of cleaning a structure and methods of deposition a capping layer in a structure. The method of cleaning a structure includes suppling a cleaning gas, including a first gas including nitrogen (N) and a second gas including fluorine (F), to a bottom surface of a structure. The cleaning gas removes unwanted metal oxide and etch residue from the bottom surface of he structure. The method of depositing a capping layer includes depositing the capping layer over the bottom surface of the structure. The methods described herein reduce the amount of unwanted metal oxides and residue, which improves adhesion of deposited capping layers.