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Pruning Perennial Flowers Most perennial flowers look best if you remove faded flowers. This is called deadheading. As a bonus, many perennials will push out another cycle of blooms after deadheading. If your perennial flowers become too tall and leggy, or flop open in the middle, try shearing them back to 6-12 inches above the ground. This type of haircut causes them to branch and become stockier.