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 or force to one or more support structures of the teeth, in a direction favorable for inducing a biological response of the one or more support structures that prepares the teeth for repositioning, for example by relaxing the tissue of the one or more support structures 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 position of a treatment stage. The primer appliances can improve the efficiency and accuracy of tooth movement by the treatment appliances.