Remove yellow calla lily foliage with a pair of pruning shears in the fall. Leave about 1 to 2 inches of foliage so you can easily see where the rhizomes are planted.
Dig down around one calla lily plant. To limit damage to the rhizome, use a hand trowel or garden fork. Calla rhizomes are planted anywhere from 1 to 6 inches deep, so adjust your digging as necessary.
Cut under the rhizome with the trowel or garden fork and lift it out of the soil.
Remove the rest of the rhizomes in a similar manner. They should be planted about the same depth as the first plant.