Abstract Two-beam systems (focused ion beam (FIB) integrated with a scanning electron microscope (SEM)) have enabled site-specific analysis at the nano-scale through in situ “mill and view” capability at high resolution. In addition, a FIB-SEM can be used to cut away a lamella from a bulk sample and thin it for transmission electron microscopy (TEM) imaging. We studied the temperature dependence of FIB milling on compound semiconductors and thin films such as copper that are used in integrated circuits. These materials (GaAs, GaN, InN, etc) react chemically and physically with the gallium in the FIB and change chemical composition and may also change morphology. Copper metallization of IC’s has been difficult to mill without undesirable side effects. FIB milling for analysis of these materials becomes difficult if not impossible. Since temperature can be a big factor in chemical and physical reactions we investigated this and report here the effect of cooling the sample to cryogenic temperatures while milling. In addition, we report on the development of a process to prepare TEM lamellae with FIB entirely in a cryogenic environment.