You mentioned doing CBT for your OCD, so I'm assuming that means you're currently seeing a therapist. If so, I would recommend talking to your therapist about your intrusive thoughts and seeing if he/she can help you get a handle on them. CBT works for compulsions and for intrusive thoughts and I know because I have intrusive thoughts, like most of us do. If you find that the therapy isn't working for you, it means one of two things. First off, maybe you need a light dose of an SSRI to help with your OCD. If you're already on a certain medication, it might mean you need to switch therapists. If you like your therapist, then maybe you need to try a different medication, as all of us respond differently to different medications.
If you do consider changing therapists, there are a few important things to consider: 1. Do they do exposure and response prevention? 2. What other techniques do they use to treat OCD? 3. Are they licensed by the Association for Cognitive Behavioral Specialists? 4. From where did they recieve their education?
Don't stay stagnant if you feel that your therapist isn't helping you out, or if you feel you need a medication change. There's no reason that any of us should stick with a therapist that we don't like, or that isn't helping us. I know it feels strange to say to a professional, hey, you're not helping me out so I'm going somewhere else, but you have to do what's best for yourself.
I would also recommend picking up some readind material. Two books I've read are both by Dr. Lee Baer called "Imp of the Mind" and "Getting Control." If you have alot of problems with intrusive thoughts, read Imp of the Mind first becuase that talks all about intrusive thoughts. After that, read Getting Control because it lists many different approaches you can take to battle back against your intrusive thoughts. It also lists different ways you can find CBT's in your area. I've also heard of the book "Brainlock" by Jeffrey Schwartz mentioned here, but I haven't read it yet.