I recently was asked about harvesting roots for medicine, the specific series of questions was about Echinacea, but the information will work for many other roots as well.
The best time to dig most roots is in the fall, after the flowers are done and the seeds are set. You need to be very careful to avoid damaging the plants crown, which is the part of the plant found at the boundary between soil and air. From the crown upwards grow the green parts of the plant--the stems and leaves. From the crown downward grow the roots. The crown itself contains the buds and tissues from which all new growth arises in many types of plants. If you damage the crown the vigor of the plant will be damaged, it will be susceptible to disease and insect infestation. So the first thing to do is to squat down and identify where the crown of the plant is.
Once you are ready to dig, you should make your cuts in the soil at least 8 inches from the crown--which will provide you with 4 inch sections of usable roots. You can make the cuts even further out if you like. Once you have dug up your plant, wash the roots well, being careful not to damage the crown. Remove roots to within 4 inches of the crown, wash them again, blot, and set them to dry on screens, or racks; out of direct sun but where there is good air circulation (so you don't get any mold). Do not bunch the roots together as they will need plenty of air circulation. They should be crisp dry before storing. To preserve the medicinal properties, for small roots it is best to store the roots whole, and then crush with a mortar and pestle right before use. (For large thick roots, it is best to slice then thinly before drying so it is actually possible to crush them once dry.)
Now, back to your plant. The crown needs protected from full sun, and drying wind while removed from the ground. Replant the crown as soon as possible after digging. If the crown is big enough--you can use a sharp garden knife to divide it to make more plants--or to make more use of the larger roots. If it was happy and pest free in the spot that you removed it from, mix some well rotted compost or manure into the hole, and replant where it came from. A layer of mulch is almost always a good idea, as is some water, unless the soil is already saturated. Don’t let the crown dry out over the next few months, and when spring comes, keep an extra eye on the plant. It will not have an adequate root system for some time, so it will need some extra attention.
Instead of digging up the whole plant you can make a cut at four inches and eight inches and remove a section of soil and roots leaving the plant in the ground. While this is less traumatic to the plant, be aware that anytime you disturb a plant’s roots you are interfere with its life and vigor, and there is a chance it will not survive.
I always prefer to use the aerial, above ground, parts of herbs whenever possible, to best preserve the plants’ lives, especially if the population of the plant in question is low. If you are interested in harvesting from wild plants, I would suggest reading a section in my book "Sacred Smoke, The Ancient Art of Smudging for ModernTimes," on 'Gathering Plants for Smudge.' The information there can be equally applied to medicinal plants. The book is available on request from most libraries and local book stores.
Questions, comments, and tips are always welcome!