Surface impurities and contamination often seriously degrade the properties of two‐dimensional materials such as graphene. To remove contamination, thermal annealing is commonly used. We present a comparative analysis of annealing treatments in air and in vacuum, both ex situ and “pre situ,” where an ultra‐high vacuum treatment chamber is directly connected to an aberration‐corrected scanning transmission electron microscope. While ex situ treatments do remove contamination, it is challenging to obtain atomically clean surfaces after ambient transfer. However, pre situ cleaning with radiative or laser heating appears reliable and well suited to clean graphene without damage to most suspended areas. Pre situ annealing of typical dirty graphe...