Hey sorry to hear about your problem.
Theres a solution you can buy from your LFS to kills cyano bacteria which won't harm any other corals or your fish. We have successfully used it to wipe out cyano that was everywhere, both on substrate and LR.
You pour the solution into your tank with the skimmer disconnected for a couple of hours. After adding the water will turn yellowish. Make sure to manually remove cyano (scraping is good enough with fingers) off of substrate and live rock as much as you can also during this time. Leave it for the night, and in the morning fire your skimmer back on. THe water will still be slightly yellowish, but the cyano will be gone. The water will go back to its normal color within the next couple of days, as the skimmer goes crazy and takes out all the extras produced by the process.
As said before, we used this method and it worked really well.
Good luck.