Describe the positions of your fortifications? As for your marksdwarf...she deserves your Baron(ess)'s chambers for essentially pulling an Audie Murphy.
It's a bunker similar to
the one in the wiki, except that I made mine "rounded" for aesthetic purposes, 7x7 with the corners bevelled off (while still ensuring no corners were open).
I built my defenses so that the only enterance was through a hole in the face of a cliff with a drawbridge. Given the direction that they were attacking from, they have to run past the bunker, climb the ramp onto the drawbridge, then keep on going past the bunker again... then they have to take on my hallway of traps to get to my wardogs and melee fighters.
(Oh, and looking back at the damage, I misread it, she actually didn't lose any toes, she only lost fingers. Her right hand is crippled, and she has at least brown damage to 4 fingers, one of them completely gone. She's basically firing a crossbow with her mouth and one thumb. My other marksdwarf on duty is... chilling at the well for no reason. I've reactivated all the rest of my military, but they're not trained in marksdwarfship, so they're going to the end of the hallway of traps.)
Seriously, though, every single shot that elite fired that didn't miss the bunker entirely went straight through the fortifications, like they weren't even there. And some of those missed shots were going completely over the bunker or not angled up at all, so as far as I can tell, those fortifications are like tissue paper.
Images (sorry if my custom tileset confuses someone):
Bunker, 2F - Enemies have to go to the west on that drawbridge to get in. There is a second drawbridge that will dump enemies into a moat still under construction:
Bunker, 1F (and goblins... the bright green one is the elite archer. The elite was firing from about where he is right now. He didn't even try to move up to get a better shot, just started firing from max range.):
Damage page (not shown: red damage to left upper arm, left hand, yellow damage to right lower arm, and grey damage to right hand) Needless to say, I'll be very surprised if she lives: