High quality thin films of topological insulators (TI) such as Bi₂Se₃ have been successfully synthesized by molecular beam epitaxy (MBE). Although the surface of MBE films can be protected by capping with inert materials such as amorphous Se, restoring an atomically clean pristine surface after decapping has never been demonstrated, which prevents in-depth investigations of the intrinsic properties of TI thin films with ex situ tools. Using high resolution scanning tunneling microscopy/spectroscopy (STM/STS), we demonstrate a simple and highly reproducible Se decapping method that allows recovery of the pristine surface of extremely high quality Bi₂Se₃ thin films grown and capped with Se in a separate MBE system then exposed to the atmosphere during transfer into the STM system. The crucial step of our decapping process is the removal of the surface contaminants on top of amorphous Se before thermal desorption of Se at a mild temperature (∼210 °C). This effective Se decapping process opens up the possibility of ex situ characterizations of pristine surfaces of interesting selenide materials and beyond using cutting-edge techniques.