Both of Canon’s big guns, the EOS-1D Mark III and the EOS-1Ds Mark III allow for lens by lens (up to 20 individual lenses – which seems reasonable) customized autofocus settings. While potentially useful for all lenses, it is particularly important for faster (f/2.8 and better) glass.

Canon outlines an iterative “point the camera and lens at a flat surface, click, check, adjust if necessary, click, check etc.” procedure. It should work. I never bothered because it seemed tedious and my lens kit is mostly the f/4 “light and good for travel” L-series. My fastest lens is the manual focus TS-E 45mm f/2.8.

Thanks to folks that understand optics far better than I, there is a second, less subjective and arguably less tedious way to calibrate your glass. This method relies on Moire patterns that result from viewing a specially constructed optical target using Liveview.

The step by step instructions are on Northlight-Images, a very nicely done site dedicated to all things Canon DSLR.

Another discussion and a similar target can be found here..