I started my H1 from Oct 1st 2012 and before that I was on my F1 OPT and did not pay any SSN or Medicare taxes.

My Employer continued not deducting any of these FICA taxes from Oct 1st.. Now when I file my Taxes and my status changed to H1 will it affect the returns in any form..

How can I pay these 3 months (Oct, Nov, Dec) FICA taxes to IRS?

Please advice.. Thanks in Advance!

You are NOT required to pay the FICA taxes; it CANNOT be done under normal circumstances.

Notify your employer in writing (email is good for this) that you were subject to FICA taxes starting on 1 October 2013, then let HIM determine how they will correct the error. Once that email is sent, you have met YOUR legal obligations in this matter.