They can't. You can put measures in place to mitigate the impact a little but without filters way up the chain and a full list of the relevant IP addresses (good luck with that), there's little that can be done aside from wondering when the relevant authorities are actually going to catch them. A sufficiently large deluge will just overwhelm whatever filter you're using. Even a very small but well crafted attack can be significantly disruptive, for example Slowloris.
The core of the problem is the availability of zombie attack hosts and the people who use them (and indeed sell on the services). Hosting companies and ISPs could fairly easily cut off a large proportion of virus infected hosts which make up the bulk of such networks (please MS, stop making insecure products). Other things like automatically blocking port 25 unless a customer requests it would help with spam too.
Unfortunately this is one area where the concept of net neutrality and unfiltered home connections leaves a barn door open.
