Heres what I'd do....
If you're moving the rock from one tank to another then before you put the rock into the new tank scrub the rock down with a brush. I had to do this once and used a new tooth brush but you may want to get a larger brush if its a lot of rock. This will get rid of a lot of the build up of algae. After brushing down the rock (or if you don't want to brush off the rock) put it in a tank (not your prized show tank) with a quality skimmer, keep the lights out and the algae (or any remaining algae) will die off and the skimmer will suck out the nutrients from the die off...
Once the algae is gone you may want to keep the lights out for a little longer (2 or 3 days) to give the skimmer enough time to do its thing.
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