Larsen likes using Mocha (bundled with CS4) for jobs involving scaling, rotation, and perspective movements. In this instance he also uses Vanishing Point to Clone Stamp in perspective in Photoshop to help paint out the lighting rig. Then he shows you the steps in Mocha, then in AE. You can download the tutorial in iTunes if you want to avoid the Cow website.
For background he also mentions a Cow article The Importance of Invisible Effects, where Steve Wright runs down a basic overview:
"One category is removing things that were needed during the principle photography, but must be taken out for the finished shot. This would include wire removal and rig removal.
The entire category of scene salvaging is dedicated to removing things that were put into the images by accident, such as scratches, hairs in the gate, light leaks, and reflections of the film crew.
Then there are invisible effects designed to dramatically change how the shot looks, but still appear perfectly unaltered, such as monitor replacement, speed changes and shot stabilization. In this article we will explore the technology and techniques that go into these common invisible effects."