A set of primer appliances and a set of treatment appliances to be worn by a subject are provided. The primer appliances are first worn to prepare the local environment of the teeth for further repositioning of the teeth by the treatment appliances. The primer appliances may apply compression to the periodontal ligament, in a direction favorable for achieving the desired final position of a tooth. The compression may generate a biological response in the local environment of the teeth. The primer appliances may cause minimal or no repositioning of the teeth. The treatment appliances are worn to reposition the teeth from an initial position to an end positon of a treatment stage. The primer appliances can improve the efficiency and accuracy of tooth movement by the treatment appliances.