Also related: Resolving That Thoughts and Perceptions are Buddha-Mind
A short excerpt from a thorough and very well written article http://www.scribd.com/doc/14021456/Thrangu-RinpochePointing-Out-of-Dharmakaya-of-IX-Karmapa
....Although one recognizes the cognitive lucidity or the lucidity of awareness within emptiness, there are different ways that this might be recognized. For example, someone might find that when they look at the nature of a thought, initially the thought arises, and then as the thought dissolves, what it leaves in its wake or what it leaves behind it is an experience or recognition of the unity of cognitive lucidity and emptiness. Because this person has recognized this cognitive lucidity and emptiness, there is some degree of recognition, but because this can only occur for them or has only occurred for them after the thought has subsided or vanished, then they are still not really seeing the nature of thought itself. For someone else, they might experience that from the moment of the thought's arising, and for the entire presence of that thought, it remains a unity of cognitive lucidity and emptiness. This is a correct identification, because whenever there is a thought present in the mind or when there is no thought present in the mind, and whether or not that thought is being viewed in this way or not, the nature of the mind and the nature of every thought is always a unity of cognitive lucidity and emptiness. It is not the case that thoughts only become that as they vanish.
The word naked is used a great deal at this point in the text. And the word naked here has a very specific and important meaning because it is used to distinguish between understanding and experience, that is to say, understanding and recognition. it is very easy to confuse one's understanding for an experience or a recognition. One might understand something about the mind and therefore think that one had recognized it directly. Here, the use of the term "naked" means "direct;" that is to say, something that is experienced nakedly or directly in the sense that the experience is free from the overlay of concepts.
Whereas normally we have the attitude that thought is something we must get rid of, in this case it is made clear that it is important not to get rid of thought, but to recognize its nature, and indeed, not only the nature of thought but the nature of stillness must be recognized. In particular, with regard to thought, as long as we do not recognize its nature, of course thought poses a threat to meditation and becomes an impediment. But once the nature of thought has been correctly recognized, thought itself becomes the meditative state and therefore it is often said that "the root of meditation is recognizing the nature of thought."
There lived in the eighteenth century a great Gelugpa teacher named Changkya Rolpe Dorje, who from his early youth displayed the signs of being an extraordinary person. He became particularly learned and also very realized, and at one point he composed a song called 'Recognizing Mother.' 'Mother' in his song is the word he uses to refer to dharmata or the nature of one's mind. This song was so extraordinary that a commentary was written about it by Khenchen Mipam Rinpoche. In this song, Changkya Rolpe Dorje makes a very clear distinction between recognizing and not recognizing the nature of one's mind. In one part of the song he says, "Nowadays we scholars of the Gelugpa tradition, in discarding these appearances of the mind as the basis for the realization of emptiness and of the basis for the negation of true existence, and in searching for something beyond this to refute, something beyond this to negate in order to realize emptiness, have left our old mother behind; in other words, we have missed the point of emptiness."
Changkya Rolpe Dorje gives another image for this mistake that we tend to make. he says that we are like a small child who is sitting in his mother's lap but forgetting where he is, looks for his mother everywhere; looks above, below, left and right and is unable to see his mother and becomes quite agitated. Along comes the child's older brother, and the image the older brother represents is both the understanding of interdependence and the recognition of the nature of thought. The older brother reminds the child by saying, "Your mother is right here, you are in her lap." In the same way, the nature of our mind or emptiness is with us all the time, we tend to look for it indirectly; we look for it somewhere outside ourselves, somewhere far away. And yet we do not need to look far away if we simply view the nature of thought as it is."...