Allow the foliage of the canna lilies to die back after the first frost. Dig the rhizomes when the foliage has turned brown and dried.
Dig up the rhizomes with a shovel. Begin digging about 6 inches from the plant to ensure you dig up the entire rhizomes and they are not damaged in process. Cutting or bruising the rhizomes allows fungus and mildew to enter the wounded area. Mildew or fungus can kill the rhizome during storage. The rhizomes will come out of the ground as clumps. Do not pull the clumps apart as damage can result. Cut off the foliage with sharp garden shears and discard.
Wash the clumps and rhizomes with a strong spray of water, rinsing off as much dirt as possible. Some of the rhizomes will separate from the others with gentle handling during the washing process.
Dry, or cure, the rhizomes for three days in a warm (60 or 70 degree F) dry location. Spread them over a flat surface. Turn the rhizomes over after 24 or 48 hours to be sure they dry on all sides.
Store in a dry cardboard box filled with vermiculite. The rhizomes should be completely surrounded by dry vermiculite, so spread vermiculite on the bottom of the box before adding the rhizomes. The storage temperature should be 40 to 50 degrees F. Replant in spring after all danger of frost has passed.