How do I proceed in filing a return for a year that had an extension granted? Is it treated as an amended return?

No, it's not an amended return. You file it exactly the same as if you were filing on time without an extension. There is nothing different in the return because of having an extension. I assume you are talking about a past year, not 2016. Except in very unusual circumstances, your extension for the earlier year has expired. But you still don't do anything different on the return. You are just filing late.

You cannot use TurboTax Online to file for a past year. TurboTax Online is only for the current tax year, which is now 2016. To file for an earlier year you have to use the CD or download TurboTax software for the year that you are filing. You can purchase a download at the following link.

http://turbotax.intuit.com/personal-taxes/past-years-products.jsp

You might get a better price from a reputable online seller that still has TurboTax in stock for the year that you need.

TurboTax does not allow returns for past years to be e-filed. You will have to print your past-year tax return and file it by mail.