Next to the option of buying the lens align system (http://www.whibalhost.com/lensalign/) which is probably the best but quite expensive tool for AF-finetuning there are several other ways to get your lenses AF properly, even perfect.
- You can find here how I did succesfull AF tuning on my tamron 28-75 F2.8
- One other method is described here: http://www.northlight-images.co.uk/article_pages/cameras/1ds3_af_micoadjustment.html