I'm not 100% sure what you're asking... but in general, rabbits like higher vantage points so I see no reason to remove a natural hill!
That said, if you're simply fencing the area in, please know that it is very UNSAFE for a number of reasons to allow your rabbits to run around like that unless a human is present to keep an eye on them. Without human supervision, they need a run area that also has a roof (to thwart birds of prey) and some sort of thwartation device (like a concrete floor or fencing that extends below the ground, probably by about a foot) to discourage/prevent digging underneath (both by your rabbits and would-be predators) and needs fencing spaced small enough to keep out snakes and such that could otherwise squeeze into the area.
As long as someone will be there to keep an eye on things, though, fencing around the area (hill and all) is good enough.