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)
you can use javascript to add in the iframe as javascript will not be indexed.
Using this method however will not only apply a "nofollow" rule but it will not get indexed as it is added in using javascript
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
include
<meta name="robots" content="noindex,nofollow">
Now, iframe that page onto the one your going to show. Easy as pie.