Keyboardhitter is right, the vast majority of meditators recommend trying to observe and let go of thoughts that pass as opposed to trying to stop thoughts. The problem with trying to stop thoughts is similar in trying to not think of pink elephants.

Mindfulness one of the key skills(if not THE key skill) exercised by meditation is the ability to be aware of one's own thoughts and feelings, and this is practiced primarily by listening to what thought's were having, and letting them go.