You need to meet with a CPA and provide all of the information you have including your return, supporting information and the notices you've received from the IRS to determine where you are in the process. It is pretty early to be dealing with issues related to 2012 taxes so it should be easier but have an experienced person look it over and determine what to do. Any notices you've received should state where to send information to. If you don't have notices the professional can call the professional services at the IRS to inquire for you.
This is not legal advice nor intended to create an attorney-client relationship. The information provided here is informational in nature only. This attorney may not be licensed in the jurisdiction which you have a question about so the answer could be only general in nature. Visit Steve Zelinger's website: http://www.stevenzelinger.com/
My colleague is correct, there is a way to go about this but it's really not a do-it-yourself area. The rules, regulations, procedures and bureaucracy are substantial. If you're able, you'll be better served to get a tax attorney involved to assist.
Evan A. Nielsen is licensed to practice law in California and handles federal tax matters throughout the U.S. The information provided here is for educational purposes only and is not intended as legal advice for a particular matter. This response does not create any attorney-client relationship with the author. For specific advice about your particular situation, please consult an attorney.