The best time to cut back lilies is in the late fall or early spring. Lilies need to die out completely before cutting them back or they may grow improperly during the next season.
While it is generally not recommended to cut back dying foliage, faded and dying lilies need to be cut or picked off the plant immediately. Leaving faded blooms on a lily flower discourages proper growth. Any dead or withered leaves should be carefully clipped off the plant without taking too many leaves off. Lilies with root rot or mosaic disease need to be removed completely from the area to avoid the spread of disease.