You might be interested in past posts on the topic:

• During the decision to create the atomic bomb, was there any thought of creating 'smart bombs' instead, to reduce civilian casualties?
  ^(19 Jul 2013 | 4 comments)
  ^(/u/restricteddata describes the targeting discussions in general.)

• TIL that Kokura, Japan was the original target for the 2nd Nuclear Bomb in Japan. However, it was too cloudy to drop it on Kokura and Nagasaki was a secondary target. Why did the Allies believe Kokura was a more valuable military target than Nagasaki?
  ^(07 Dec 2014 | 121 comments)
  ^(/u/restricteddata discusses the Nagasaki situation specifically.)

If you have followup questions, feel free to comment with them directed towards an expert with a mention.