How can you stop Nature's Prophet from doing his thing every game?

Nature's Prophet is very easy to gank while he is jungling

Spirit Breaker, Bounty Hunter, Clinkz, there are countless heroes that love eating that big fat creep.

Nature's Prophet can't really do much besides split push

His teamfight contribution never really becomes that much. You will thus have an upper hand in any team fight that occurs.

Don't try to chase Nature's Prophet that much

He needs to come at your towers to do anything, wait for that, rather than go for these weird hunting missions I see some people do. You are just wasting time of everyone on your team, Nature's Prophet can Teleportation  around the map faster than you can chase him anyway.

It's a good idea to have someone expendable to go greet Nature's Prophet every time he gets close to pushing down your tower. Someone with plenty of counterpush, like Keeper of the Light or Lina. Nature's Prophet can't really do much about this

Wards and dewarding are pretty important

If enemy Nature's Prophet can see that area he TP's to is safe, you're making the game easy for him. If you can't see the area he TP's to, you are making the game very easy for him. Getting a gem to deward enemy vision, rather than to catch Shadow Blade Nature's Prophet, is a good idea.

Keep lanes pushed beyond the river if at all possible

That way, any time you start fighting, Nature's Prophet can't just TP next to your tower and take it down. This goes with map vision: You can't safely push lanes without vision of the enemy and their movements.

Clockwerk + Gem of True Sight

Is Nature's Prophet off alone pushing down one of your towers. Hookshot in on him before he even sees you. He will Sha dow Blade to try and escape. It doesn't matter; you have a Gem of True Sight. You're still hitting him. He is cogsed, he can't run anywhere. He is making a futile attempt to teleport away but battery assault keeps cancelling it. He is dead.

After two or three times this happens he will probably give up.

Bounty Hunter

Generally you are in the offlane which can make it hard for you to get experience sometimes when the wave pushes up or is pulled back to the enemy tower. Why not use this time to roam invisible into the jungle and find Nature's Prophet to shut him down early. You can't necessarily kill him but you can pop out of invis to steal his last hit on that big creep; hit him a few times and then run away... Heck, maybe you can kill him. He is alone and if he tries to teleport away you can break it. Later in the game when he has his Shadow Blade you can keep jumping up to kill him. Make sure you get your Track off first and he can't run away.

Clinkz + Dust of Appearance

Clinkz is great at punishing people who stray away from the pack. Wait for him to be alone and then pop up behind him, strafing him down, bursting a Dust of Appearance so he can't run away. Watch his trees burn.