Simply shrink your enemies using the Shrinker and walk up to them to step on them. Repeat 39 more times. The Shrinker is the silver-ish looking ray type gun with a green cell in the middle of it. You first acquire the Shrinker on Episode I Level 4, in the part when you need to slide a card (red card I think) and then it reveals the shrinker, and you need to get to the other side of a small passage. You can shrink any enemy, including the alien pods or eggs. There are two good fast ways to do this.
1. Start up "It's Impossible" in Episode IV and get the Shrinker at secret 3. Save it here and then use the 10 shots. Load your save when you're out of ammo. It saves ALL kills.
2. Start up "Duke Burger" in Episode IV and go to the back to the drive through and press X on the menu, then jump on top of it and grab the Shrinker and blue key card in a compartment which opens, save and do the same as the above step.