If there are no fish in the tank, suck as much water out as you can, below the gravel line. Then refill by pouring the water slowly onto a plate on the substrate. This will suck all the "fines" down into the bottom of the substrate. Other than that, a good deep gravel vacuuming when doing water changes for the first month or so will make most of it go away. That's what I did when I didn't rinse it well enough, it never makes mud anymore. Good luck.