That's just algae. If you have a good skimmer, you can stir your sand to get rid of it but don't go deeper than about 3/4" the bad stuff hides about 1" down. If you just agitate the top layer, you won't cause any harm, but it's still messy. The more simple solution, but also more expensive is to just use natural sand stirrers to do the work. Look at Nassarius snails, sand sifting stars, fish like jawfish and gobies, or some conch's. They will constantly turn over the top layer of sand and help to keep it clean. I would start with 2 stars and 10-15 snails and see how it goes from there, or as I mentioned, there are several fish that will help with it too but a fish alone won't do much good. You do need to make sure that your rock work is stable before adding any sifters to your tank though. As they burrow beneath your aquascaping they will create pockets that can lead to an avalanche and a broken tank. Most of us place the rock directly on the bottom and then add the sand around it to prevent this problem. I am using silicone to hold my base rock before I put any sand in mine. Some people just use pvc to make little stands. You can do it several ways, just make sure you aren't set up for an avalanche if your rocks move a bit...