Change material of only one instance of a prefab

Hello,

i have a prefab of my alien enemy. During the game i spawn these aliens in waves like:

 GameObject clone = Instantiate(enemy_prefab, Spawnpoints[i].transform.position, Spawnpoints[i].transform.rotation) as GameObject;                        
 ++enemyCnt;
 clone.name = "Alien" + enemyCnt;

During the game i need to change the material of some aliens, but everytime i change one, the material of ALL aliens in the scene changes. I really don't know how to handle this since i try it for a very long time now. It is no problem to change the color of a single alien, i have just problems in changing the materials.

Thank you for your answers!

*edit:

The idea behind the game is, that the enemies are invisible. You have a gun with two modes - deadly and paint. It works to map the paint onto the aliens when the renderer is off. So when i hit an alien i want it to flicker so the player can see the shape of it. Therefore i made a glass-like material. The actual problem is, when i start the flicker method of an alien - all aliens are flickering. Here is the code i wrote:

In Update Method:

 if(flickerSequence > 0)
 {
         flickerTime -= Time.deltaTime;
 
         if(flickerTime <= 0)
     {
       if(flickerSequence % 2 == 0)                               
              setMaterial(MATERIAL.INVISIBLE);
           else
           {
               if(!DEBUG_MODE)     
                   setMaterial(MATERIAL.NONE); 
               else  
                   setMaterial(MATERIAL.DEBUG);
           }
 
          flickerTime = FLICKER_INTERVAL;
          --flickerSequence;
 
         }
 }

When i want it to flicker i set flickerSequence to the value how often i want it to flicker. This is how the material is changed (or the visibility state):

 public void setMaterial(MATERIAL type)
 {
     //Debug.Log("Switching alien material of " + name);
 
     switch(type)
     {
        case MATERIAL.DEBUG:
          renderedObject.renderer.material = debugMaterial;
          renderedObject.renderer.enabled = true;
          break;
        case MATERIAL.INVISIBLE:
          renderedObject.renderer.material = invisibleMaterial;
          renderedObject.renderer.enabled = true;
          break;
        case MATERIAL.NONE:
          renderedObject.renderer.enabled = false;
          break;
     }
 
     actMaterial = type;
 }