I'm a software engineer who used to work in Defense.
I previously had a Top Secret SSBI security clearance.
As such, the FBI has my finger prints on file.
I remember when I was investigated for the clearance I was told that I could have the finger prints expunged in the future.
I no longer do classified work and I don't like the government having my finger prints on file. How do I request the FBI to remove my finger prints from their files?

You don't, once in the system your fingerprints will always be there.

There is no reason to "erase " them, they are there for ID purpose. Anyone fingerprinted, from boy scout leaders, to gun owners, to those fingerprinted for job purposes are all put on file for reference