In meditation you are simply observing the mind and body as it is experienced in the moment. If they happen to be lost in illusions of different sorts, then your job is merely to trace, in real time, the course of the illusion, to experience its comings and goings, rather than try to get rid of it. At least that's one approach to meditation.
In the world of mental health and psychiatry the use of brain scans is often highly suspect the data from them is often been manipulated to support weak theories about mental illness. Still, neuroscience is exciting and the developments that are happening are certainly fascinating. It's a good idea to approach any reports that use brain scan data critically and carefully. This article in the Guardian brings up some good things to be aware of when considering any reports that use brain scans to support their claims.