Probably he was fingerprinted in that apprehension, which is what led to his identification in the Montgomery, AL case.
Note that the Montgomery police in all likelihood ran their single fingerprint sample against local and FBI databases, and they came up empty.
Yet when the Feds ran the print, they identified Malvo.
My guess is that the Feds (the sniper task force) gained access to the INS fingerprint database, and used it, while the local Montgomery, AL police had no access to INS fingerprint records.
I suppose that INS fingerprint records are not normally shared with the FBI or any other national fingerprint system, due to "privacy" concerns.
How utterly disgusting.
Check this out...
Suspect left danger signs in Bellingham
(FBI had Terror Tip on Sniper
Muhammad, October, 2001!)