As Étienne said, the optimal transformation (perspective correction, that is with trapeze deformation) is slightly complex and hard to do by hand. However, it can be easily modeled with matrix operations (assuming the lens deformations are corrected beforehand) so that software can work with them. The difficulty is to find the right matrices, especially in our classical case where cameras were not calibrated (the calibration works only if the cameras and their focal are fixed), which is usually done by finding a bunch of homologous points and solving an optimization problem to align them as much as possible (with correctly found [and well placed] homologous points, sub-pixel accuracy is achievable).
His software is great for that.
It also has an automated batch mode, though the interface to reach it is a bit complex (several conditions to make it appear in the menu that pops if you click at the right place if I remember well ; refer to the online doc).
It's too bad that it needs some minimal developer skills to install it. It's a break for a large adoption of it by the stereo enthusiast community.
Actually, it is far easier than it was some months ago ;-) but it could probably be improved more.