how to freeze/null a scene when a pop up GUI is active please help!

Hello I was wondering if anyone could help me or point me in the right direction. I have a countdown timer pop up in the UI goes from 3 2 1 then disappears to the level as shown:

The only problem is, I can still click and interact with the level despite the countdown going on. Is there a way (a script) that temporary freezes/nulls everything so I cant click and interact until the countdown goes away? The countdown has an animator attached and the scripts I have are:

using UnityEngine;
using System.Collections;

public class CountDown : MonoBehaviour {

	public bool counterDownDone = false;


	
	}

and this:

public class SetCountDown : MonoBehaviour {

	private CountDown GMS;

	public void SetCountDownNow ()
	{
		GMS = GameObject.Find ("GameManager").GetComponent<CountDown> ();
		GMS.counterDownDone = true;
	}

If anyone could help me I would greatly appreciate it!! Thank you!

Does anyone else know any scripts that would help me in this situation? I would GREATLY appreciate it! Thank you.