It is a program to match records of aliens entering the US with records of aliens leaving the US through the matching of biometric identifiers such as fingerprints, iris scans, or facial recognition.
The program has been in development for a long time, since it was recommended in 2004 by the 9/11 commission, and the relevant portion of the EO is essentially an instruction to the Department of Homeland Security to get its act together.
See http://thehill.com/blogs/congress-blog/homeland-security/266341-why-is-the-biometric-exit-tracking-system-still-not-in.
Most visitors are already fingerprinted and photographed when they enter the country, but exit records are collected by airlines rather then government officers, and no biometric identifiers are taken when they leave.
Modifying the system to add exit checks by CBP officers would require a good deal of construction at most of the country's international airports, as well as a significant increase in the size of CBP's force of immigration inspectors.