This post is long and may be confusing…I apologize ahead of time.
Background: I have just got into this hobby about 3.5 months ago and I am learning quickly. Tank has been up 3.5 months. Fish have been in for about 2 months now. Water parameters are good. I did start hitting the tank with chemicals about 7 days ago now (reef chemicals like iodine, kent nano reef A & B ,etc) but followed the directions exactly.
I am 80% certain that my clown fish has black spot disease (Black Ich). He matches pictures on the internet of it and I found him scratching (at least that is what I think he was doing)last night. Bad pictures of my fish can be found at Picasa Web Albums - Justin - fish (if you use the magnify option you can see the black spots). They have doubled in number since I took these pictures about 36 hrs ago. I will try to get some good video of the spots on youtube later this afternoon and will update the links on this post Other then what I think was scratching (he was shaking very fast in the water last night 3x but not up against anything but he did the same thing once in the sand making a small hole all within a 5 minute window) he is acting completely normal. I am going to pull him out of my main tank (29 biocube ) and put him into QT for a copper treatment (can’t treat my main tank as I have corals and crabs). Getting him out should not be hard as he is very curious and will probably come up to check the net out. . I am 100 % open if anyone has any other ideas, suggestions, alternate diagnosis.
In the main tank I am going to hit it with a UV sterilizer and Ich attack Kordon LLC - Kordon - Herbal Ich Attack . Yes I know that it these methods will not kill it completely but IMHO it is better than nothing at this point.
If it is black spot disease the clown fish is not my big problem….
I have a lawnmower blenny in my tank and he has no signs of the disease what so ever as of this morning. Getting him out of the tank will be next to impossible. Has anyone heard of blennys getting black spot disease? It is my understanding that black spot is not as aggressive and deadly as regular marine ich and it tends to attack tangs more than anything else.
To top this all off I leave for a 10 day business trip on Wednesday…talk about awesome timing.

This is a good synopsis and indicates how to eradicate the parasite.

What is Black Spot Disease? - Reef-Fanatics.com - The Authority In Coral Reef Keeping And Saltwater Aquariums

Good luck.

__________________
Doc

Dr Hank's 200 gallon Reef Tank
http://www.aquariumforum.com/f46/drhanks-tank-3440.html