you could just use the Destoy() command? I guess you have a 'if' statement for the GUI.Button,- you could just take the box as a 'Var : GameObject' and then set the 'if' statement to destroy it if the right button is pressed:

 `if(GUI.Button("Rect stuff here"))
  {
   //The cube is a varible
   Destroy(cube);
  }`

If you need something more flexible, then you can create Functions:

 `function DestroyObject(object:GameObject)
  {
     //the '5' is how long you want to delay the Destroy command
     //(it only works for the destroy command)
     Destroy(object,5);
  }
  //now declare that in the 'if' statement
  if(GUI.Button("rectangle stuff here"))
  {
     //again, cube is a varible defined elsewhere 
     DestroyObject(Cube);
  }`