At one point, my back glass, sand and rock were all covered in a thick layer of chrysophytes. It has been a long slow process, but they are almost gone from my tank now. The first thing I did was to greatly up the flow in my tank. I also greatly upped my maintenance routine (changing filter socks frequently, cleaning out the skimmer daily, maintaining stable parameters, etc.) That got rid of the stuff on my sand in pretty short order, and has kept it from growing back on my glass after manual removal. It did little to affect the stuff growing on the rocks though, so I cut my light schedule back to one hour per day. I don't have any corals in this tank yet, so I don't have to worry about affecting them fortunately. I maintained this schedule for quite some time, and could see the chrysophytes slowly getting thinner and receding. Recently, I started gradually increasing my light schedule again. The lights are currently on for five hours per day. The chrysophytes are not completely gone yet, but they still seem to be receding. I scrub some off every so often, and let the overflow send it to the filter socks just before I change them. Everyday I can see more and more bear rock. I will be adding a UV sterilizer soon that I hope will help prevent them from coming back. I also want to try inoculating the tank with some coraline soon to see if I can jump start that growing in the tank while the chrysophytes are weakened, and hopefully out-compete it for substrate.