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If it's a DSB (deep sand bed) you're not supposed to clean it. If it's a shallow (eye candy) sand bed, you can use a gravel vac to clean it, pulling out the water that you replace in your water changes.
Manually removing the biopsis infested sand is the best method to get rid of it. I've done this by scooping it out with a net. If the aquarium is newly established then I'd recommend just trying to get out as much as possible by hand as frequently as possible and just hang in there. These things tend to pass if you are dilligent.