it sounded like you didn't intend to remove the whole colony. Now that it's out you can trim to your hearts content...afterwards why not reattach the left over colony back onto it's base?
Personally i don't like the look of spreading epoxy/putty over rock. What i do where possible is to chip it away. I have to do this with my invasive encrusting montis. I got a 24" flathead screwdriver and lighty tap the handle with my frag cutter or other small cutters ( don't use a hammer). this usually does the trick. Just watch out for rockwork that isn't secured...