I do the same with 20 strand brass wires, usually take them down to 12 or 14 strand.
If you gently wiggle them around at the ends where they're soldered, eventually they'll give and they usually come out super clean. If they don't you can use a thin file on them just to be safe.
As for taking out outer or inner wires... it's just up to preference. I find that if you take out more of the center-most wires, you get more buzz but less initial punch, and vise-versa if you take out the outer-most wires.
The only thing you have to make sure about is that you take out the equal amount of wires from each side obviously.