I've never been able to permanently get rid of the cyano that appears on my sand. (I have large fish, and they eat a LOT) However, I can control it. What I do is vacuum the sand bed every now and then, and immediately follow the vacuum by 24-36 hours of darkness. I find that really knocks it back and it will remain gone for quite a while.
The darkness doesn't seem to bother any coral or fish. Sometimes, I'll even feed the fish a bit during the dark day.
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400 gal reef. Established April, 2007. 3 Sequence Dart, RM12-4 skimmer, 2 x OM4Ways, Yellow Tang, Maroon Clown (pair), Blonde Naso Tang, Vlamingi Tang, Foxface Rabbit, Unicorn Tang, 2 Pakistani Butterflies and a few coral gobies
My Tank: http://www.canreef.com/vbulletin/showthread.php?t=28436
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