most parasitic worms are invisible to the human eye. Most likely it is fly larva of some sort.

Only way to be certain your guinea pigs don't have internal parasites is to take fresh samples of poop to your vet for a fecal.

Having to clean them twice a week, seems to me excessive, unless the cage is rather small for the number of guinea pigs you have. I kept 3 guinea pigs together in a large pen and it only needed cleaning once a week.

What size cage do you have and how many guinea pigs?
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PHLdyPayne