They would destroy the two military targets with precision strikes, in the same way as the modern day military would. While debating the atomic bombs is outside the scope of this thread, I'd emphasise I think it was probably the right call to drop them in those unique circumstances. The US military DID NOT choose the two cities in question because of a specific military objective, though like most cities in any nation in WW2 they contained significant military targets. They were deliberately left off the target lists for 20th air force firebombers partly with the "testing" of the atomic bomb in mind. In fact Nagasaki wasn't even the the first choice target, Nagasaki was added to the target list after Kyoto was removed, because of its cultural significance, and on the raid itself it was only a backup for Kokura. Revisionist historians sometimes describe the atomic bombings as unnecessary or even as war crimes. They ignore the two main reasons that everything was done at the end of WW2 by the USA, to just end the constant deaths of its citizen soldiers ending a war that could only end one way, and to say to the USSR "keep off the grass". Back on topic, while the darker actions of Section 31s attempted genocide, Sisko's environmental pollution (though the episode suggests that no deaths were involved) and probably other examples suggest the Federation is not squeaky clean, as a policy they would never force an unconditional surrender through the carpet bombing of civilians. The main reason being, they don't need to. Area bombing in WW2 was not a choice, the technology existing at the time meant the only way to guarantee dislocation of industry was to carpet bomb an area hoping to take out a factory and those who worked there. As a concept, while vastly more effective in Japan's wooden cities than it was against Germany, area bombing proved less effective than anyone ever hoped, and would prove ineffective again in Vietnam. Modern day estimates suggest an F-16 armed with JDAM or similar smart munitions has the ability to affect targets equivalent to 100 B-17s, due to the accuracy of its weaponry. Starfleet could easily destroy a military target in a city without affecting any surrounding civilian targets, so why bother nuking anything?