Pellican cases and the like. They have three layers of foam. The center foam piece is to be cutout to fit the firearm/accessories.

 Does anyone have a method to do this neetly?

what i did was place firearm on center foam, get a Sharpie marker and draw outline of firearm.

Pull center foam out of case and place on cutable surface ( i jus used cardboard)

I used a 4" benchmade knife , what ever ya use it has to be razor sharp, the foam in the pelican case is kinda hard (texture) so with a sharp knife it cuts easily, the trick is to make sure ya cut ALL the way to the bottom, the foam is pretty thick, and i jus use a delicate sawing action, try not to PULL the foam with the knife or it will tear and look like ass.

Three options that I know of to make it easier
1. Freeze the foam.  Kinda hard if you're trying to do a rifle and don't have a big freezer.
2. Electric knife.  You know, the carving knife you got as a wedding present?
3. Build a "hot knife".  There's instructions on the web how to make a knife out of a battery and some stiff wire. for example, this one:
wolfstone.halloweenhost.com/HalloweenTech/fotmak_MakingFoamTools.html#AssortedTools

Pelican's instructions say to use chalk for the outline and and electric carving knife to cut it. I'll be doing this myself when my AR10 gets here.

if it's closed cell foam (harder stuff), you can heat seal the cut surfaces with a heat gun (even a hair dryer)

this will fix a lot of errors.