[From a teaching on The Treasury of Eloquence: Lord Guru Omniscient of the Three Times and Lord Vajradhara given by Bardor Tulku Rinpoche. Translated by Lama Yeshe Gyamtso. Transcribed by Pat Ahearn. Edited by Matt Willis. All rights reserved. Please do not reprint without permission. The complete teaching is available as an MP3 download from the KPL Bookstore.]
The problem we have is not that thoughts arise. Thoughts arise because they are the natural display of the mind’s nature. The problem is that we do not let thoughts just be. We always try to do something to them. We are so habituated to this that we may not even notice it; we may think of it as natural. But, in fact, it is not natural.
We constantly follow thoughts. We invest in, are captured by, good thoughts. We invest in, are captured by, bad and neutral thoughts also. When we do this, we sully the mind. Just as if you put your hand in a stream or river and agitate the water you will stir all the silt up from the stream bed and the water will be temporarily deprived of its natural pellucidity.
So the answer is to accept the mere appearance of thoughts, and just let it be.