Meditation is that state of mind where we often tend to relax our body and mind by engaging in a peaceful, calm and silent state. It triggers the highest points of our brain to  make them calm & relaxed. It does not always mean to work in a systematic and rhythmic manner; but it keeps going through twists & turns. We cannot expect our mind to  not think anything; he thoughts flow into our system without our permission. 

Whenever we sit down to meditate, there is bound to be a thought process going on inside our mind, some thoughts will come and go, we may regulate them to a certain limit. But there is no particular 'topic' about which we must think while meditating.

Though what we can try is to circulate our mind towards nothingness; where there is nothing & everything- this state of mind is called entering our soul through our body. Remember that our body is a pathway to enter our soul. We could utilise it if we want.

This will not happen immediately, but eventually with time, we may notice this new kind of experience. 

Also read: http://answers.mindstick.com/qa/35857/what-does-meditation-do-to-your-brain-mind