according to some bleeding edge research, a thought is really just "memories", or mental echoes, which come together from various regions of the brain of various conscious experiences. Recall a very clear and distinct memory you may have. Now try to remember different things about this experience: was it hot or cold? what color shirt were you wearing? remember any smells?
Junctions form between bidirectional, neural pathways, which come and go to and from the different region of the brain, each region has its own functions: limbic system=emotion, sensorimotor cortex, hippocampus=learning and memory, etc. When you experience something the neural circuit(path) of your sensory perceptions junction with learning neural circuits, impulses at this junction cause an association to be made and a biological torrent is created, and stored, which is basically a memory trace of the various information from the different parts of the brain. When you remember something, in your brain the activity is the same as if you were really experiencing it. So, what is real then?
This does not answer the philosophical question though of "thinking matter".