Brian Roemmele answers this question on Quora:
I began to wonder how would Apple secure such an important piece of biometric data. Working in the payment card business for over 30 years and in particular with the encryption requirements for PIN numbers, I knew that there could be no software only solution for this problem. Thus I always knew that there would be a need for a segregated area to encase this data in hardware.
Apple not only has developed one of the most accurate mass produced biometric security devices, they have also solved critical problems with how the data from this device will be encrypted, stored and secured. Apple Calls this the Secure Enclave and it is a relatively new concept.
There are dozens of applications and use cases on the roadmap and I am certain a developer economy will build around this amazing technology. One that is very clear is retail payments and Apple will have quite a number of unique ways they will solve real problems for merchants and iPhone users. I can say this aspect of Touch ID will be more magical then what we have seen thus far. There will be connections to iBeacons and the amazing technology Apple just acquired through Passif.