Yes. The initial proposed target, in 1943, was the Harbor of Truk, which was essentially the Japanese equivalent of Pearl Harbor — a totally military target (not a military target embedded in a larger city). There were studies for awhile at Los Alamos on using atomic bombs against harbor targets, but they seemed to make it all too complicated. For a variety of reasons, by 1944-1945 their approach had changed towards targeting cities and the atomic bomb's technical characteristics seemed to lend towards that as well. By the spring of 1945 they were explicitly talking about targeting cities and urban areas.

But it is interesting and important than the alternative was considered, and considered well before cities became the target. Later the research that had started as a result of the Truk possibility became part of the work that went into the 1946 Operation Crossroads nuclear test series, which looked into the effect of nuclear weapons on naval vessels.

For a very thorough discussion of this, see Sean Malloy, "'The rules of civilized warfare': Scientists, soldiers, civilians, and American nuclear targeting, 1940–1945," Journal of Strategic Studies 30, no. 3 (2007), 475-512.