The first time after you restart an iPhone 5S you have to enter your PIN and can't use the fingerprint scanner. Seems like a good security protection. The same thing happens with App Store purchases, the first time after a restart you have to enter the password.
What if that's not just a second security check. It would be super smart if the PIN and password were only ever stored in the "secure enclave" part of the CPU, so in memory and never written to disk. Even if someone got the iPhone and took it apart to get at the memory chips, they couldn't get the PIN or password.
You'd have to somehow tear the CPU apart while the iPhone never turned off.