I have implemented this in my Final project, you buy SDK of your thumb scanner, or it would be free with your thumb scanner driver, then do work in C# and connect C# with mysql, connect php with mysql and communicate among both languages.
Another way is to use C++ language, use SDK C library and work in C++, pass the object to php using connection bw C and php.
I believe PHP cannot directly deal with any hardware, leave aside the scanner. Rather, the actual scanning and verification must be via a native language like C or VB. So the scan results are 'passed' between them and the PHP code...