I was in US on H1B visa from 2011 to June 9 2014. I filed my 2014 returns from India through online software which filed it as 1040 with status married filing Jointly.

Now, I have read some posts indicating that I should be filing 1040NR as I was not present in US on last day of the year. Hence I should amend using 1040X and file a 1040NR instead.

Issue is that 1040NR has to be filed with status married filing separate. Hence following questions -



Which form should I use to file my returns - 1040 or 1040NR
If 1040 NR I should amend my returns - but as per IRS guideline, I cannot change my filing status after April 15 filing deadline. So how can I file 1040NR with different status?
My wife also had some income with federal tax withholding and she must file amended return as well. Now, with 1040NR, our tax liability is higher and hence part of the refund we received must be paid back - how do we divide the refund on the joint return to the separate returns?

Your filing of Form 1040 online is okay IF you included ALL of your Indian income earned in 2014. You would also file Form 1116 to claim the Foreign Tax Credit for Indian income taxes paid.

You also need to submit a Residency Termination Statement, to be mailed to the IRS NLT 30 June 2015.

If you need professional help with this, email me at the email address in my profile.

I haven't included any Indian income after I came back to India as I considered that would be taxable only in India. Also, I guess as per the treaty rules, I might qualify as Indian resident than a US resident and hence I feel I should file 1040NR.Given this, can I still file amendment for both of us and file 1040NR with status married filing separate? Would that be accepted as it is changing the filing status.And, if I file 1040NR, do I need to send any Residency Termination Statement?

If you do not file as a resident and include all world-wide income (and file Form 1116 to claim the Foreign Tax Credit for Indian taxes paid), then you would a expatriate dual-status return, while using Form 1040NR to calculate the taxes.

The dual-status return is NOT for amateurs; get professional help from someone who has experience filing dual-status return.

And, yes, the Residency Termination Statement is required irrespective on how you file.