Haresh:
The start-up company has a legal obligation to provide an up-to-date summary of your salary, either with pay stubs or some type of printout that shows what they have paid you year-to-date. Just ask your employer for the summary/printout and why you need it. I would be shocked if they are not tracking your pay using some type of payroll/spreadsheet program.
At the end of the calendar year, they will provide you with a W-2 or (more likely) Form 1099-MISC, showing you to be working as an independent contractor.
Yes, you can and should file your tax return using Form 1099-MISC. You would have to file Schedule C with either the Form 1040NR/1040NR-EZ (if you file as a non-resident alien) or Form 1040 (if you file as a resident alien).
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