Taken from http://homeguides.sfgate.com/cut-lily-stems-44256.html
Lilies continue to use their stem even after the flowers die. Garden lilies (Lilium spp.) offer a variety suitable for almost every climate and garden design. Most types blossom in summer, producing large flowers atop tall stems. Lilies grow from a bulb that collects and stores nutrients for each season's growth. The stems play a vital part in nutrient collection, which requires careful cutting when you clean up the plants or harvest flowers for indoor display. Clean tools and proper timing further ensures that your lilies remain healthy and productive for many years.
Garden Maintenance Cut through the stem directly below the swollen base of the lily flower when the petals begin to wilt. Use sharp, clean shears to make each cut. Leave the green stem on the plant. Shear off the stem when it begins to die and turn brown or yellow. Make the cut where the stem emerges from the base of the plant. Remove the cut stems from the garden, and compost or dispose of them. Leaving dead plant material around the base of the plants may invite disease organisms or pests into the bed.
Cut Flowers Examine the lilies and locate stems where the flower buds are just beginning to open but have not yet opened completely. Selecting buds not fully opened helps ensure the longest blooming period as a cut flower. Support the stem just beneath the flower bud with one hand. Cut through the stem with a sharp knife two thirds up its length from soil level. Place the cut flower stem in a bucket of lukewarm water immediately so that the bud has continuous access to moisture. Cut off the bottom inch of the stem at a 45-degree angle before placing it in its permanent vase. Cut down the remaining stem in the garden after it dies back naturally and is done collecting nutrients and energy for the lily bulb. Hope this helps you with how to dead head lily plants. Till next time, this is Becky Litterer from Becky's Greenhouse, Dougherty Iowa