you will never be able to totally get rid of all the shrooms if they have taken over every thing, the only way to insure you kill all of them is to boil all the rocks in your tank...and i do not reccomend doing that enless you want to start all over anyways, if all you have is shrooms get a shroom eating nuddy
cant starve a shroom of light and kill it eather, i had live rocks in my garages in holding tanks without a light tht had shroom on it for 7 months and the shrooms servived, they where pretty clear looking but they got there color back after the rocks went back into a tank...they where the purple ones also