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Meditation is non-distraction
Thoughts stay usable
Thoughts still arise, and they remain usable. A person doesn't become irrational or less intelligent, and all the usual tools are still there. The difference is that everything is in plain view.
Thieves and empty houses
A Tibetan Buddhist analogy compares thoughts to thieves entering an empty house: there is nothing for them to steal. In the usual case something really is in jeopardy. Every thought ends the meditating, and most of the time the thinking itself feels terrible, so it is understandable that thoughts seem like a problem at the start.
Focus as training
Some kinds of meditation treat thoughts explicitly as a problem, because the practice is to focus on one thing to the exclusion of everything else, thought included. That training can be good to do, and it becomes a tool for other kinds of insight.
How do traditions split focus from insight?
Buddhist traditions distinguish samatha, a calm and concentrated mind held on a single object, from vipassana, which observes whatever arises. The Theravada texts describe the two as working together. Tibetan traditions use the terms shine and lhaktong for the same pair. In both cases, concentration is treated as a base that steadies the mind for insight practice.
Does meditation change how the brain handles thoughts?
In a 2011 study in Proceedings of the National Academy of Sciences, Judson Brewer and colleagues scanned experienced meditators and novices. The meditators showed less activity in the default mode network, a set of regions linked to mind-wandering and self-referential thought. They also showed stronger connections between that network and regions involved in cognitive control. These differences held across several kinds of meditation the group tested.
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