The dark web is like a lair for hackers/criminals/etc.
That's an oversimplification, but we'll go with it.
But has anyone, like FBI or CIA ever found the main server of the dark web? Where is the main server located? I thought all Internet data flows are being watched by many government institutes like FBI/CIA. Why have they not chased the main server of the dark web itself?
I mean the dark web is actually a part of the "healthy"/"surface" web right ? why they did not get caught by the main server provider ?
We apparently need to cover a broad number of basics here.
First, there is no main server of the public web. That is not how the web works. I can't go into that much detail in an SE answer, but your computer generally uses (the distributed) DNS to turn a human-readable hostname into an IP address, and then that gets routed across physical wires based on (again, distributed) routing protocols and data until it gets to the server it's supposed to get to.
The so-called dark web is structured similarly - different people run different web servers, and traffic has to go to the right places. The difference is in how you get there.
There's an anonymizing technology called Tor. When used to connect to the public web, a tor user's traffic goes through three different intermediate servers before trying to get to the requested website. The first node knows who the user is, but not what they were requesting (it's encrypted). The third node knows what's being requested, but not who requested it. And the middle node knows essentially nothing. This process prevents the website and other MitM snoopers like the NSA from knowing who is requesting that website.
(Insert a bunch of caveats here around anonymity with tor, attacks on the protocol, safe browsing, and general advice to please go look up more than this comment before relying on it.)
Tor also provides a feature known as hidden services, where the website operator also sets up a circuit of three nodes to connect to. A tor user's circuit meets up with the website's circuit, and traffic flows through all six of the nodes without anyone knowing who the other parties are. This is how the deep web works.
The only question then is how the two meet up in the first place, and that uses yet another distributed piece of technology, a distributed hash table built into tor. So there's no centralized server to shut down here, either.
The weak point here is that the website operator needs to not leak their identity or the server's location on accident, which can happen through all sorts of misconfiguration or human error. But even if they do, that is only that one site that gets shut down, not some giant shutdown of the network. Also, anonymity is not illegal, so there is no legal reason for the feds to shut down tor overall, even if they could. It in fact started as a US government project to assist people in oppressive regimes.