Advanced Cloning With After Effects

I know how to get a fairly good looking cloning shot when the camera is on a tripod during filming. But I'd really love to know how to do it the way this guy did, with the camera handheld. Here's the link to the video:







I really don't understand how it is possible to clone like that; Does it have something to do with motion tracking? Any help would be very much appreciated!

Thanks :)

thanks for your fast response :) It's not really specific enough for me though, I'm really not an After Effects pro, I am only able to do basic things... Thanks for your help anyway though! :)