I enrolled my 2 year old in GE and at the interview they didn't fingerprint him. The reason given was that up until the child is 12-13 years old, their fingerprints can't be accurately read by the machines. They told me that upon entry, to swipe my son's passport and I would get a printout with an 'X' on it. I should take the sheet to the front of the line and give it to the next available agent who would process us through.

It's not a secondary inspection - just has to be handled by a live person though.

As an aside, I also enrolled my 13 year old and he was in fact fingerprinted at the interview.