Disclosed are embodiments of an ion beam sample preparation thermal management 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. The shield has features which enable the durable adhering of the sample to the shield for processing the sample with the ion beam. The complementary datum features on both shield and shield retention stage enable accurate and repeatable positioning of the sample in the apparatus for sample processing and reprocessing. A heat sink means is configured to conduct heat away from the sample undergoing sample preparation in the ion beam. The ion beam irradiating means may modulate ion beam intensity between at least two intensities. The shield retention stage may be stationary or rotating.