I keep thinking that the best way to defeat Dooms is not with brute force but with brains...this is how Batman beats characters wwaaayyy more powerful than he is. The Surfer will have to fight smart, not just big. All attacks I've read about so far have taken place on a classical-physics level. On the quantum level, all material is equal; no substance is more/less indestructible than the next. And because of the uncertainty principle, it would be straining belief (at least mine, anyway), that Dooms could adapt to an attack on that level.
Then again, the Ultimate Power is, as always, the Writers. If they want DD to be like pre-crisis Superman--Flat-Out Unbeatable--then so be it.