I haven't been doing much research in the past year and don't have much experience with Native research but my wife did have a couple of family lines that made applications to the Mississippi Choctaw. Here is how I used to access their applications at Fold3/footnote.

1. Log onto your personal Fold3 account.
2. Goto to this link at accessgenealogy.com (free site) and enter your ancestor's name and tribe too if you know it in the "Search the Final Rolls by Last Name" dialog.

http://www.accessgenealogy.com/native/finalroll.php

(In this example I used surname Zeigler and tribe Choctaw and clicked search).

3. You are taken to a page with a table of people. (For this example click on the "MCR5052" link in the "Card" column.

4. You taken to a page titled "Dawes Commission Case Files" on accessgenealogy.com. Further down the page there is a dialogue box titled "Search Dawes Footnote". Click the "Search Button" for this dialog and you will be taken to the the application images on Fold3.

NOTE: This technique only works if you have a personal subscription to Fold3. It doesn't work if you're accessing Fold3 with a library editions as far as I know. Also, the applications images are all online for free at www.archive.org but site is not easy to navigate unless you already know what you are looking for.

Ron