Depending on your situation you have a few options.
#1 Is really simple but if your gonna have more than a dozen or so links on the page or multiple pages of dynamic links it not an ideal solution.
Simply create a modal for each iframe link and put the iframe code in the modal. Then mark each link with the correct modal class.
#2 is a little less simple to setup and will require a small snippet of jquery added to your js files.
Basically you make one modal with an iframe in it with an empty src attribute.
Then make your links point to the URL you want them to open in the iframe and add the class for your single iframe modal to all links you want to open like this.
So all links will have class of say eModal-1
In your js something like this assuming your jquery version is v1.9 or above.
jQuery(document).ready(function(){
jQuery(document).on('click', 'eModal-1', function(e){
e.preventDefault();
jQuery('#eModal-1 iframe').attr('src', jQuery(this).attr('href'));
jQuery('#eModal-1').emodal('open');
});
})
This basically says all links with class eModal-1 when clicked the modals iframe will change to the target of the link and then open the modal.