What I think you're asking is if you can file a physically separate tax return. If your business is a sole-proprietorship or single member LLC, then no, you can't do that. You'll report it on a SCH C as a part of your personal tax return.
If your business is a multi-member LLC, partnership, C-Corp, S-Corp or joint venture, then you *have* to file a physically separate tax return using TurboTax Business (different from Home & Business).
The self employment taxes do show up on a separate line on your tax return. But it is included in your refund or Tax due. Self employment and schedule C is a disregarded entity and goes on your personal tax return. If you have a Net Profit on schedule C you get social security credit for it and can use it as income to contribute to a IRA.
Why do you think you want to file it separately?
I was assuming the question was for the same reason I see this question all the time. Folks mistakenly believe that if they file their business as a separately taxable entity, it will reduce their tax liability. What most don't realize, is that it has a greater potential to actually increase that tax liability - even if the business operated at a loss.