Leaving a mark after clicking

First of all, you must find the 3D point clicked, what you can do using Raycast. You may have a mark object - a sphere, for instance - and move it to the hit point, like this:

 var mark: GameObject; // drag the mark object here, if any
 ...
   var ray = Camera.main.ScreenPointToRay(Input.mousePosition);
   var hit: RaycastHit;
   if (Physics.Raycast(ray, hit)){
     if (!mark){ // create a sphere if no object assigned yet
       mark = GameObject.CreatePrimitive(PrimitiveType.Sphere);
       mark.renderer.material.color = Color.green;
       mark.collider.isTrigger = true; // make it a trigger
     }
     // move the sphere to the clicked position
     mark.transform.position = hit.point;
   }
 ...

You can create the mark object and drag it to the field mark (a green sphere will be created if there's no mark object assigned to mark)