The solution depends on the cause.
- you can only raise (or dig) so far. So if the original ground was not level (it was not, unless you are building in an area smaller than 1 floor tile). then raise everything to the max will be ... just as uneven as the original.
in that case, you knock everything down to the lowest common level, or insert an extra stone floor tile or two in low spots.
other causes ... mostly see above...