Howdy smoorman, I would not recommend removing roots. If You are using a submersible pump in the reservoir, there are available water pump filter bags that will help keep the roots from clogging up the pump intake. I use a piece of rolled up fiberglass window screen around the reservoir drain valve to keep the roots from getting into the valve. The root will follow the flow (if any) of the water in the system like the pump intake and the flow from the irrigation lines at the bottom (or top) feed to the planter cubes. It is not a great problem because by the time the roots get that well developed, the constant irrigation is not needed as much as when the plants a new.