If you are on an F1 Visa and only in your 3rd year, you would fall under the 5 year nonimmigrant exemption still. This means you will not file a US Resident 1040 return until AFTER the 5 years has been met. When your 5 years is up, that is when you would start counting the days to meet the Substantial Presence Test. When you meet the Substantial Presence Test, then you would file a 1040 form as a US Resident.
Until then, if you have income that you are earning in the US, you would need to file a Form 1040NR which TurboTax does not support, however our partner Sprintax.com does.
Since your spouse does not live in the US, she would not meet the substantial presence test to file as a US Resident. Since neither of you meet the conditions to be a US Resident for tax purposes, neither of you would file a 1040 form. If she has US Sourced income, she would also need to file a 1040NR. As to which filing status, as non-resident aliens, this question would be best asked of Sprintax.com since they specialize in Non Resident returns.
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