If i understand your question correctly then you want to really apply a no follow on the links that are inside the iframe?
Personally i would have said this to be more a job on SO then webmasters however, i'm not sure on an exact way of doing this but these may provide a temporary fix but you may want to investigate them before trying.
- My first approach (but not sure this is exactly what you are looking for)
you can add rel="nofollow" onto an iframe like so
<iframe rel="nofollow" src="http://mysite.com">
- My Second approach (i think this would again not be your ideal)
Another alternative is from this post
This was the top result page#1 on Gxxgle and it had not been answered
as of yet. How sad. Absolutely, you kind of can add rel="nofollow" to
an iframe. You just must be tricky about it. Here's how... Build a
blank html file. Add your iframe to that alone. In the Meta tag
<meta name="robots" content="noindex,nofollow">
Now, iframe that page onto the one your going to show. Easy as pie.