Disclosed are embodiments of an ion beam sample preparation apparatus and methods for using the embodiments. The apparatus comprises an ion beam irradiating means in a vacuum chamber that may direct ions toward a sample, a shield blocking a portion of the ions directed toward the sample, and a shield retention stage with shield retention means that replaceably and removably holds the shield in a position. The shield has datum features which abut complementary datum features on the shield retention stage when the shield is held in the shield retention stage. A retention stage lifting means allows the creation of a loading chamber that is isolated from the main vacuum chamber where sample ion beam milling takes place. A heat sink means is configured to conduct heat away from the sample undergoing sample preparation in the ion beam.