Im not sure that he wants to take something that looks like a link and actually make it into a link...
From my understanding, he wants to make something printable...and make a sort of footnote effect, in essence, everywhere in a certain document a url appears replace it with some sort of notation, in his case [1], [2], and so on, and take the link that was removed, and put it at the bottom of the page with the same reference next to it...
at the bottom
[1] : [url]http://....[/url]
[2] : [url]http://....[/url]
Theres no point in making them clickable if this is a "printable" version of the same page