I was under the impression that he implies they use Extremis at the end of the movie as well up until 10 seconds ago when Tets mentioned the unreleased subplot
Either way it makes the most sense that he would use Extremis to assist in removing the shrapnel. It's pretty much what happened in the comics and it would be kind of weird if he didn't end up using Extremis to remove the shrapnel in the you know... Extremis movie..
Either way with the direction the Iron Man movies and Avengers 1 took with the progression of the Iron Man suits it's still likely we will say the Extremis suit in either the later half of Avengers 2 or at some point in Civil War or Avengers 3. It would be really really weird if they didn't go in that direction given all of the steps already taken. Not to mention Tony will need it in order to not get completely smacked down by later villains like Thanos and even to an extent Ultron.
End of the day in my headcanon with the way the final scene is presented and worded it just makes sense that he used Extremis in some fashion to help remove the shrapnel and will later on use it to become the Iron Man suit.