triggermen
1. How long do you have him? A fish this big, if caught wild at that size will takes weeks to become acustomed to captivity.
2. Why did you take out the rocks? Was it to 'prevent' the fish from hiding? If so, you really need to do a bit of research into fish behaviour - especially fish like angefish. An emporer angel MUST BE ABLE TO HIDE. If not he will get very stressed, and sooner or later will die. To be happy they need to be able to get out of sight..... they need a spot where you cannot see them, and they cannot see you. If you provide plenty of cover, the fish will settle, he will colour up and become much more "at home"...... and eventually will be very tame. My 6" emproer will attack my arm - he has no fear of me at all!
3. Is it you he is hiding from, or is he trying to hide all the time? If you creep into the room, very quietly, is he out swimming? If so, its just you he is afraid of, and in time (if you let him settle) he will calm down and realise that you are not going to harm him, and then he will be very tame.
HTH
Matt