This study used the power of neuroimaging to identify the neural systems that remove information from working memory, a thorny issue to examine because it is difficult to confirm that individuals have actually modified their thoughts. To overcome this problem, brain activation as measured via fMRI was assessed when individuals had to clear their mind of all thought (global clear), clear their mind of a particular thought (targeted clear), or replace the current thought (replace), relative to maintaining an item in working memory. The pattern of activity in posterior sensory regions across these conditions confirmed compliance with task demands. A hierarchy of brain regions involved in cognitive control, including parietal, dorsolateral prefrontal and frontopolar regions, were engaged to varying degrees depending on the manner in which information was removed from working memory. In addition, individuals with greater difficulty in controlling internal thoughts exhibited greater activity in prefrontal brain regions associated with cognitive control, as well as in left lateral prefrontal areas including Broca’s area, which is associated with inner speech.