Accessing script variables of instantiaded prefab

Hi guys. This is one of my largest problems - I never know how to access specific parts of my object, and it seems that every time I have to use a different method. I am posting my current problem here, but would be glad to receive a longer explanation of this component hierarchy.

My code: A spawner object spawns a prefab from a prefab array. (this works fine)

 Transform enemy = Instantiate (prefabs[size],transform.position,
                               Quaternion.identity) as Transform;

Afterwards I want to set some attributes of the instantiated prefab. All of the prefabs have the same script attached "Enemy.cs"

 public class Enemy : MonoBehaviour {
     public Attributes attributes;
 }
 
 [System.Serializable]
 public class Attributes
 {
      public float xSpeed = 10;
      public float ySpeed = 10;
      public float size =0;
 
 }

The way I set the atributes is by creating a new object of Atribute class and assigning it to the script. There is a function in spawner that returns a randomly generated attribute object. So what I am trying to do in code looks like this:

 Enemy enemyScript = enemy.gameObject.GetComponent<Enemy>();
 enemyScript.attributes = MakeRandomAttributes ();

The first line of this part throws an error. (Object reference not set to an instance of the object). I did something similar witha bit different architecture and something similar worked fine.

What am I doing wrong? What is the difference between GameObject and Transform?