To remove the many little lakes that might be generated, use Tools>>Global Set>>Water Level Value with a value of 0. This action puts the level back to the original sea level (0).
You get lots of little lakes because fractal functions have hills and valleys at all scales (self-similarity sorta dictates that). Post-processing such as filling basins and so on works well, but you're limited by practical resolution issues.
One thing you can try is to eliminate the fractal function and use FT as a simple heightfield editor like Wilbur. You'll be limited to the editing resolution of your world, which is a bummer. The "Burn Into Surface" option evaluates the world, places the results into the offset channel, and sets the roughness to 0, effectively removing the fractal function contribution. Fill basins should then fill basins exactly and not have the problem of slight variations causing little lakes everywhere. As always, try this on a COPY of your .ftw file, not on the only version.