ISO files are basically DVD images; the GameCube, in fact, uses Mini-DVDs, with work the same as normal DVDs (exept they are smaller).

For this tutorial, some files may be needed, GCTool and GCRebuild.

To extract files from GCN ISOs, you must open GCTool as admin, and open up your Paper Mario TTYD ROM, after doing so, it should look like this:

Now create a new folder somewhere, and on GCTool, go to ISO>Extract whole ISO. Now select extract also Header and AppLoader, press Choose DIR, select your newly created folder and Extract. This might take 5 minutes. You are now ready to follow any tutorial where a not ISO ROM is needed.

If the instructions wern't clear enough, here is a GIF to show you what to do:

This part is easy, just open GCRebuilder, open the root folder where your modified rom is, go to save and then rebuild.

Here's the GIF on how to do it: