Hi I have been looking at the eagle schematics for the cobra and was wondering if it would be possible for me to have the .lbr file for the EMX module?

Why do you need it? Just use the one from the schematics you have.

I am designing my own board for the EMX module and it would be alot easier with the correct foot print. Is there a way of removing the footprint and placing it in a new project without the original library file?

You can extract lib from schematics but you do not need that. All you have to do is cut/paste the EMX module from Cobra into your design.

Or just take the cobra design files and delete everything while leaving the EMX module.