You can use a global variable to stop/start the timer
I did an example of that for someone else -
In that example you press go to start the timer and stop to stop it. The timer counts upward instead of down, but the principle of stopping/starting it is the same.
You would need to check that there are no enemies left to kill and then set the global variable that controls the timer to false/off
If all enemies are spawned at the start just do System->Compare Two Values->Enemy.Count = 0 (where Enemy is the sprite/family of the enemy objects)
If enemies are spawned over time, use a global variable to track how many enemies are killed (Enemy->On Destroyed : System->Add 1 to EnemiesKilled) and compare that to a variable used to track how many Enemies are to be spawned that level.