Lois, since the market for biometric authentication is not as vast as, say, cd-rom burners, you are probably going to have to use the packaged software that comes with the fingerprint reader. I can't see why you wouldn't want to. If you feel you can write a better API via PHP, it would mean you have more resources for R&D than the few biometric companies in the world.
As you probably already know, even with the R&D that companies or governements can put into biometric authentication, the hardware requires tuning to avoid false positives. From the reader, the credentials need to be transferred to the database of fingerprints to perform a match. There are various ways of doing that, but I think that IF you were to do it with PHP, it would have to be with PHP as some sort of wrapper.
Like planetism, I am not aware of any PHP APIs already available for such a thing. If security is of such high concern, there are so many other languages probably better suited than a scripting language like PHP. I love PHP, believe me, but you don't use a mallet when what you need is a sledgehammer.
