Assuming that you are an employee of an organization you need to fill either ITR-1 form or ITR-2 form(which one depends on your rebate claims, show your Form-16 to some expert). You will input the details of your Form-16 in this ITR-1/ITR-2. Whether you do online or offline filing, you need not attach your Form-16.
The last date of income tax filing is already over. If you have not submitted your IT return you will have to do it now with fine.
In any case you need not submit Form-16 anywhere.
Please note that from this year, online filing was compulsory for the people whose income slab is above 5 lakhs. So please consult with your nearest CA who does return filing at the Income Tax department. He will do the necessary things for you.
With Best Regards,
and once you file your income tax return yourself through their easy step by step guide then you will not miss any step to file your return in the most professional manner.