Do you have a legal separation in your state? There are a few states in which legal separation is not recognized. What state are you in?
You can file as single if you are "legally separated from your spouse under a divorce or separate maintenance decree." That means a decree from a court. As xmasbaby0 said, not all states have legal separation. Check with a lawyer.
If you are legally separated according to the IRS definition, then the IRS considers you unmarried. In that case, you cannot file as married filing separately and neither can your ex-wife.
If your state does recognize legal separation, then you can amend the prior two years and claim single status. make sure to include a full explanation for the amended returns. something like. I'm changing my filing status from married filing separately (MFS) to single. My spouse and I are legally separated under the laws of the state of ________ therefore, I am no longer considered married under the US tax code since ___________ (enter date of agreement).
you may even want to attach a copy