work around for transforms on Instantiated prefabs

Hi, I'm currently trying to make a simple tower defense game and i want my enemies to follow a set path in my game. I'm using an array of transform positions to achieve this. However when i try to save this to a prefab it doesn't save the transforms, so my instantiated enemies don't move when they spawn. Have know idea where to begin to solve this. Thanks!

 #pragma strict
 var forwardSpeed : float= 1;
 var health : float = 100;
 public var waypoint : Transform[];
 private var pointA : Vector3;
 private var currentWaypoint : int;
 var levelMaster : LevelMaster;
 
 private var maxHealth : float = 100;
 
 function Start () {
     levelMaster = GameObject.FindWithTag("LevelMaster").GetComponent(LevelMaster);
     
     forwardSpeed *= levelMaster.difficultyMultiplier;
     health *= levelMaster.difficultyMultiplier;
     maxHealth *= levelMaster.difficultyMultiplier;
 }
 
 function Update () {
     if(currentWaypoint < waypoint.length){
     var target: Vector3 = waypoint[currentWaypoint].position;
     var moveDirection : Vector3 = target - transform.position;
     var velocity = rigidbody.velocity;
         if(moveDirection.magnitude <1){
         currentWaypoint++;
         }
         else{
         velocity =moveDirection.normalized * forwardSpeed;
         }
     }         
     rigidbody.velocity = velocity;    
         //transform.Translate(Vector3.forward * (forwardSpeed * Time.deltaTime));
         
 }
 
 function TakeDamage(damageAmount : float)
 {
     health -= damageAmount;
     if(health<= 0){
         levelMaster.enemyCount--;
         levelMaster.enemyCount+=(maxHealth + forwardSpeed*levelMaster.difficultyMultiplier);
         //levelMaster.UpdateHud();
         Destroy(gameObject);
     }
 }
 
 function Slow(){
 
     forwardSpeed *= 0.5;
     yield WaitForSeconds(1);
     forwardSpeed *= 2;
 }