This paper examines copper-interconnect integrated circuit transmission electron microscope (TEM) sample contamination. It investigates the deterioration of the sample during ion milling and storage and introduces prevention techniques. The paper discusses copper grain agglomeration issues barrier/seed step coverage checking. The high temperature needed for epoxy solidifying was found to be harmful to sidewall coverage checking of seed. Single beam modulation using a glass dummy can efficiently prevent contamination of the area of interest in a TEM sample during ion milling. Adoption of special low-temperature cure epoxy resin can greatly reduce thermal exposure of the sample and prevent severe agglomeration of copper seed on via sidewall. TEM samples containing copper will deteriorate when stored in ordinary driers and sulphur contamination was found at the deteriorated point on the sample. Isolation of the sample from the ambient atmosphere has been verified to be very effective in protecting the TEM sample from deterioration.