How do you negate an EPM?

This is the very question I'd like answered. You see I'm writing a book and need to know what stops an EPM wave, field or blast, to better protect the Empire's ships from attacks.

the year is 2563 but any sort of anti EPM knowledge will help.
Check out the series "Jericho." If you don't know the series here is a little spoiler, the US is attacked by EMP bombs that burns all electrical equipment but one guy has a laptop incased in a shielding metal brief case (it is probably the same idea as the Faraday Cage.

Another possible example is in Matrix when they 'zap' the machines with their EMP but to do it they have to turn all electrical equipment so that they wouldn't fry their equipment as well.