This sounded hokey to me at first, but my therapist told me to practice naming those thoughts in my head, and then moving past them. So when I have an obtrusive thought, I take a deep breath in and hold it (creating tension in the body) while I say to myself, "I acknowledge that I'm having an obtrusive thought." Then I slowly exhale (releasing that tension, slowing the heart rate) and say, "Now I'm letting it go."
Like I said--I was convinced that this would not work, until I tried it. It's amazing how well it *does* work, for me!