ISAPI rewrite does not (can not) change the physical HTML code, but what it can do is convert the request into something else. For example we have links like this:
<a href="/widgets.cfm">Widgets</a>
<a href="/gizmos.cfm">Gizmos</a>
and in our rewrite rule file, we have:
RewriteRule ([^\?]*)/widgets.cfm$ $1/categorypage.cfm?id=100 [L,QSA]
RewriteRule ([^\?]*)/gizmos.cfm$ $1/categorypage.cfm?id=101 [L,QSA]
So that a request for http://www.ourdomain.com/widgets.cfm actually requests http://www.ourdomain.com/categorypage.cfm?id=100, so in other words, we have SEO friendly URLs like widgets.cfm instead of URLs with parameters (?id=) in them. That is how the URL is "rewritten" in this context. Both URLs would work, but we never expose the one with the parameters to the end-user. URL rewriting is an entire subject in its own right, and is not directly related to ColdFusion as it works with all server-side languages.
Solaced, can you give an example of the URLs you are working with, and what you need the outcome to be?