Hard to say what organism is growing on your rock without a microscopic look at it. If it is a diatom reducing silica will help, otherwise if it is an algae, reducing silica will not help.
There is no miracle cure for algae, dinoflagellate & cyanobacteria & diatom pests in a reef tank.
The bottom line is that you want to reduce nitrate, phosphate, dissolved organics and suspended organics. You need to say no to all pests present in your tank and all debris in your tank. Keep a spick and span tank including the sand bed and glass. This will need to be completed often to erradicate these type of pests.
There are a lot of hobbyists in your same position. Reducing your nitrate and phosphate levels to a zero reading will help in getting rid of many type of algae and/or cyanobacterial pests. IME, reducing nitrate and phosphate levels too low can kill or cause problems for many types of soft coral. Running GAC & GFO will all help in reducing the growth of these type of pests. In many cases they will not eradicate the pest even when phosphate and nitrate are extemely low. Vinegar and/or Vodka dosing will help reduce the nitrate and phosphate levels also, but will not necessarily eradicate the pest either.
A common problem is being able to identify your pest to a category correctly: true algae, cyano, dino, bacteria & other assorted pests that look similar. In many cases a micro look at your pest is best to properly ID it to one of these categories.
IMHO, if you are faced with an algal type pest problem, it is best to implement an algae pest control program strategy:
1) Wet skimming with a good quality skimmer. Clean your skimmer cup at least once per week.
2) Reduce your nitrates and phosphates to a zero reading using the hobby grade test kits. See Randy's articles regarding this:
Phosphate and the Reef Aquarium
http://reefkeeping.com/issues/2006-09/rhf/index.php
Nitrate in the Reef Aquarium
http://www.advancedaquarist.com/issu...t2003/chem.htm
3) Proper lighting. I find that the higher wavelength bulbs are less conducive to algae growth. I now run 20,000 K bulbs from using 10,000 K bulbs.
4) Proper day length is a good thing also. I would not run your lights for more than 12 hrs total. Keep in mind that light entering from a window nearby is added to this figure.
5) Running GAC is a good practice in my book. It will help reduce the total dissolved organic carbons in your tank water and this is a food source.
6) Proper 30% per month total water changes will help export the DOC as well as some of the pests in the water column. It will help maintain the micro-nutrients as well.
7) Physical removal of the pest by hand, scrubbing and siphoning is important as well. If the amount of pest in your aquarium is overwhelming, perhaps dealing with one section at a time is a better idea.
8) Proper water circulation in your tank to prevent dead zones. When dealing with cyanobacteria pests increasing the flow where it grows seems to help.
9) Use RODI water for all top-off, salt mixing, additive mixes... etc.
10) Dosing iron may have benefits for macro-algae, but if you are experiencing algae pest problems than I would stop dosing it as it can add to the problem in many cases.
11) If you are dosing other supplements such as vitamins, amino acids, or others that contain a mix of supplements other than the basic alk., calcium and magnesium, I would stop these until you gain control of your pest. This includes many of the store bought products with unknown ingredients. Dosing Vodka or vinegar to reduce your nitrates and phosphates would be an exception in my opinion.
12) Proper feeding habits. This can be the number one problem when trying to reduce your nitrate and phosphate levels. Use low phosphate fish foods.
13) IMHO, lighted refugiums may be a problem when trying to deal with an algae type pest problem. They are wonderful when it comes to reducing nitrates and phosphates. However, the light over most refugiums is conducive to the microalgae type pests. If the refugium becomes infested with a microalgae pest, I would clean it throughly of all pests as best as possible, remove the macro and turn off the lights until you gain control of your pest. Re-using the same macroalgae later may serve as a source for re-infestation of your pest.
14) Adding fish and other creatures that will eat your algae pest will help.
15) Running a diatom filter which has been suggested by Boomer, makes a lot of sense to me. It will help remove a lot of organic material in your water column.
16) Keep your sand bed clean if it is a shallow bed weekly by vacuuming it. Lightly vacuume deep sand bed surfaces.
17) Keep your tank glass clean all the way around regularly. Perhaps it will need to be done 2 to three times a week if growth is fast.
18) For some additional thoughts regarding switching an algae based system to a bacterial based system see this thread:
(Using a carbon source with appropriate bacterial dosing may possibly help to push your system to where you want it although this is controversial.)
http://www.reefcentral.com/forums/sh....php?t=1781320
19) There are other items that can be added to this list if others care too share and some of the items listed may be disputed.