Form 8843 should be filed separately since it is handled by a completely different department than the regular 1040NR.

Also remember to include:

• Form 8316, including a statement of why the employer cannot refund the incorrectly withheld taxes
• A copy of the filed 1040NR
• A copy of the students' form I-20
• Copies of any W2
• A copy of the students' visa
• A copy of the students' I-94

This is all handled by the IRS service center in Ogden, UT by the Business International department. You can send it to Austin and they will forward it or you can send it directly:

Department of the Treasury

Internal Revenue Service Center

Attn: Business International

Ogden, UT 84201-0038

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Their processing time for these requests are about 1 year right now so expect for quite a wait to get the refund, however since this could add up to quite a lot of money it is worth waiting for.