Take preventative measures to protect your orchids roots from rotting. Rotting roots is a very common problem with orchids and many other types of plants. Root Rot will usually affect plants that have been newly potted the most. Over watering the plants can be a big cause of root rot on your orchids. Be sure to only water your orchids the recommended amount of water for the type of orchids you are growing.
Also, the type of pot you are using can have a big impact on your orchids with regard to roots rotting. Do you use pots that drain well with lots of holes to allow air to circulate through the potting mix? Or is your pot one without holes? It is best to have a pot that allows air to circulate through it and also one which has holes on the bottom so that the excess water can drain. This will help prevent root rot on your orchids greatly.
If you notice your orchids roots are already rotting there are a few things you can do. You can re-pot your orchids immediately. While you are repotting the orchid scan the roots for the ones which look like they are dead or decaying already. If they are not plump, healthy looking then use a sterilized pruning shear, knife, or scissors and trim them off. By doing this you allow your orchids healthy energy to flow to the healthy part of the plant and not be wasted on the parts of the plant which are dead already.