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cleaning substrate

Hi. I am wondering if there is a good method for cleaning substrates in 
heavily planted tanks. I am having a very difficult time vacuuming my 
fluorite because my tank is carpeted with crypts.  I believe that my 
thus mulmy substrate is the major cause of an ongoing green water 
problem ( I don't feed much, do large volume weekly water changes, use 
CO2/trace elements, limit light to 10 hours/day, have a clean up crew of 
snails/ghost shrimp helping out). 
Thanks, Laurel