Pruning your herbs is important to keep them growing and healthy in your indoor garden. You can start pruning when the plants are about 2 inches tall. Follow the main stem back to the previous leaf set and cut right above the 5th set of leaves. Cut the herb back about 1/4 inch above a node (the place where leaves come out). Leave a few inches of leaves (3 pairs recommended) on the plant after pruning. Never take more than 1/3 of the plant when pruning. Pinching or cutting back basil plants regularly encourages full, bushy plants. Trim a basil plant every two to three weeks and pinch off the flower buds as soon as you see them.