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For reference, I worked for 4 months at an internship in Massachusetts in the summer of 2016. I'm a Canadian citizen/resident, and don't pass the substantial presence test for 2016.

Is there anywhere to include the possibility that I overpaid for Medicare and/or Social Security Tax in my federal or state (Massachusetts) tax? Or should I be using it as a deductible on my Form 1040NR-EZ?

I've seen that workers on a J1 visa are exempt from these taxes also, but is there any analogous rule for someone on a TN visa if they don't pass the substantial presence test?

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Nonresident aliens in certain statuses are exempt from FICA taxes (Social Security tax and Medicare tax). TN is not among them. Your FICA taxes were withheld correctly; you did not overpay (unless you worked for more than one employer during the year and exceeded the Social Security tax limit for the year).

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