If there are 2 units that are 3 might attacking a battlefield and the enemy has 1 unit at 3 might and they do counter strike preventing an instance of damage does the unit still die

No — your 3-Might defender survives: Counter Strike prevents the entire combat-damage instance dealt to it, so all 6 Might from the two attackers is prevented and nothing is marked on it (CR 438.2, 438.5.b; FAQ #9605).

The attackers still have to assign that damage to it — the assignment happens, the damage just gets replaced with 0 (CR 438.5). Note the key point is that combat damage to a unit is one simultaneous instance, not one instance per attacker, so Counter Strike isn't "used up" by the first attacker only.

Your defender isn't prevented from dealing damage, though: its 3 Might must be assigned lethally-in-full to one attacker first, so one 3-Might attacker dies (CR 467.2.c.3). That leaves both players with a unit at the battlefield → No Result, and the surviving attacker is recalled to your Base, so you keep control of the battlefield.