Why would doctors remove an atypical nevus?

Reduce cancer risk. Skin cancers like melanoma are totally curable when they are caught early enough. Changes in moles signal a possible start of skin cancer. If the doctor is not sure. Or if he/she is sure. The best policy is to remove the mole. After it is looked at by the pathologist, it can be determined if it is cancerous. Which may require a new surgery or not cancerous in which case it is now gone.
Atypical Nevus. Atypical or dysplastic nevus has the ability to turn into a melanoma. The best way to minimize that risk is to surgically remove the whole nevus.