1) Ensure that you have either your EZ Gun (If you're playing in Very Easy), MK22 or M1911A1 equipped.
2) Sneak up to an enemy from behind. Be sure to sneak up to the enemy using the D-Pad, as this guarantees that Snake moves at a pace that which doesn't generate an excessive amount of noise. If Snake moves too quickly, the enemies may hear his footsteps and Alert mode may be triggered.
3) Once you're very close to the enemy (say about a few feet or under a meter away), hold down the Square button. Snake should stick out his gun at the enemy's back and the enemy should stick his hands in the air.
The trophy should unlock a few seconds afterwards.