I putting in a 100amp sub panel. I know you have to keep the neutral and ground separate in the sub panel. BUT there are two neutral bars one on each side in my GE box. My question is can I take the bar out that connects the neutral bars together, use one for equipment grounding and the other for neutral.

I think I can ONLY IF the one I use for ground is bonded to the panel

I personally wouldn't do it because it makes the wiring messy.

Look for a green screw that may need to be removed when using this box as a sub-panel. This isolates the neutral. But then you need the ground bar kit.