I just posted a response to a question similar to this on another topic... heres what I wrote, only edited a little
----------------------
Heres what I'd do....
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. 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) make sure you have 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.
------------------
In your case I would keep the lights out even longer. From the pics of your tank I saw it apeared you didn't have any corals (except some nice aptasia). Try keeping the lights out about 2 weeks longer than you think it would be ok to turn them back on..
HTH.