Since the DOM tree of a page is active and always reflected in the browser, what is the best way to modify this DOM tree for some purpose without affecting the actual render
Maybe consider one the many great JavaScript librarys out there, e.g. jQuery. These allow you to easily copy parts of or even the whole DOM of an document and have that stored appart from the DOM.
If you need to roll your own solution, a good point to start is Resig's post on document fragments: http://ejohn.org/blog/dom-documentfragments/.
Good luck.