This work explores the challenges associated with studying the microstructural properties of REBCO-based coated conductors by transmission electron microscopy (TEM).This review highlights the crucial role of focused ion beam (FIB) lift-out technique via scanning electron microscopy (SEM) to be accurate during the preparation of thin lamellae.Challenges associated with FIB preparation, especially for multilayered materials, are thoroughly discussed, and potential solutions are proposed.The essential aspects are the chemical removal of the copper, silver, and superconducting layers before lamella preparations and the sensitivity of the silver protective layer to ambient conditions and beam irradiation.Furthermore, the study of the different etching processes for TEM lamella preparation also explores a new method for the recycling of single-crystal substrates.