Ok, I have tried to recreate what you want to do, heres a tutorial:
I will be showing you how to smooth the part in green on the gun, then you can do that for the rest of the gun.
Right click on the gun and find "Chamfer Edge" (Shown in the picture)
Select the 4 edges that you see (actually you only see 3) To get it to go into wireframe, Right click on where it says "Perspective" in the top right of the small window which is near "Top" "Front" "Left" ect.
Hold the mouse down on those 4 edges, and it will "Split" them into 8, smoothing them down.
Repeat this for all of the edges on the gun, making them smooth and nice
Create the mesh for which you will cut out on the gun, as shown as the blue mesh.
Move the trigger template mesh into where you want it to cut out
Go to Objects > Compound Objects (as shown in the picture)
Click on the button that says "Boolean" (shown in the picture)
Click on "Pick Operand B" Then click on to what you want to be cut out, which is the trigger mesh (the blue model)
It should now have cut it out, if it hasnt then say and I will tell you how to fix it.
What you should do is this in reverse order, first cut out the trigger, then smooth down the gun. And this is what you are left with:
