Failing to control the flow of our thoughts can impact our success in everyday life, and it is characteristic of multiple psychiatric disorders including depression and post-traumatic stress disorder. It has been demonstrated that thoughts can be removed from working memory (WM) in three differential methods (i.e., replacing a thought with something else, suppressing a specific thought, and clearing the mind of all thoughts), which recruit distinct neural regions involved in cognitive control (Banich et al., 2015). Our research has focused on how these different removal operations impact representational changes in WM and WM capacity as a result of the changes. In our removal task, participants were presented a target picture (a face, a fruit, or a scene) and then performed one of the removal operations based on a given instruction after the item offset. Employing multi-voxel pattern analysis (MVPA) on fMRI data, we were able to demonstrate that replacing, suppressing, and clearing are distinct neural processes that act upon WM information in different ways. By tracking the information contents of WM during the removal operations, we found that replacing an item was the quickest way to diminish information, followed by clearing and then suppressing. However, the representation of the removed item was mostly altered in WM when it was suppressed, followed by clearing and then replacing. Furthermore, these operations had different impacts on the encoding of new information. While maintaining an item interfered with the encoding of the next item as predicted, only suppressing an item, which displayed the most alteration of that item during removal, led to release from this proactive interference and even facilitated subsequent encoding (Kim et al., 2020). These results suggest that removal operations modulate WM representations in different ways, resulting in distinct consequences of representational alteration and WM capacity.