I'm not aware of being able to do this, but I think it would be good to be able to exclude files/folders when making an ISO directly from a CD/DVD.
I'm specifically thinking of removing ei.cfg from Windows 7 DVDs, without going through the rigmarole of copying the files to C: drive, deleting ei.cfg and remaking a bootable ISO, using someting like nLite (which doesn't actually support Windows 7 anyway).