For a few of my games what i do is this:
Hero hero; //User
ArrayList<Aliens> aliens //ArrayList of enemies
Lets say I want to check if they are colliding!
for(i = 0; i < aliens.size(); i++){
Aliens a = (Aliens) aliens.get(i); // <-- This might be something you want to do
if(hero.getBounds().intersects(a.getBounds())
kill();
else
a.remove(i);
}
Now this is just an example but I am sure you should be able to use this in your program! I could help a bit more if you could provide more of your code!