Be more specific...
What do you mean... a mess? Do you mean detritus and debri settling at the bottom of the filter? I wouldn't take it offline as it can affect the cycle and dirty your tank up. Try adding a powerhead at the bottom to lift the detritus off the bottom. What type of filter is it?
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30g reef tank, CPR CY192 filter w/ DIY plumb running Rio 17HF return, Coralife 3x 9w UV Sterilizer, 3 24W T5-Helios 10K Daylights/3 24W T5-Helios Blue lights, 2 Logysis blue meteor light strobes (moonlights/24 Blue LEDs).
Tiger tail cuke, asst. snails/hermits, asst. feathers, rainbow acan,zoos,shrooms,bubble,galaxea, asst. shrimp, 2 ocellaris,mandarin,zebrasoma xanthurum,pink-spot watchman,red-striped pistol. | 
Wet Dry 
jb
