The best answer is: Remove the soil and roots from the raised bed and put down a layer of landscape fabric, being sure it folds up and covers the sidewalls by several inches. The fabric will allow water and air to move through the soil, but it will prevent the pecan roots from invading your garden. You could continue to plant in the bed with the tree roots present, but the tree will always be more successful in accessing the water and nutrients than the vegetables you plant.

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