Hello DrewsBrew,
Welcome to Cartographer's Guild!
World building is a massive and complex topic. The way I see it you have a large set of choices to make about how you go forward with developing the world. From the simple where it looks right at this point in time, to the complex where you can tell someone how mountains formed and which tectonic plates have moved where since the world's crust became stable. There are a number of software tools which will throw out randomly generated world maps (Fractal Mapper for instance) but I'm not sure how much history they take into account. I'd be tempted to go the manual route of super-continent + tectonic activity + time(erosion) = current landmasses. This way you can tell where mountains will be due to plates pressing up against one another. Mountains can also be formed by tectonic hot-spots creating active volcanic mountain ranges.
As for the places which have never been besieged due to natural defenses... I would think it would be a game of disincentives where the possibility of a successful siege was so slim that no-one felt inclined to bother with the attempt in the first place. The problem with that is you don't (generally) get history written about sieges that never took place. I think you're more likely to find historical references to places which resisted siege for extended periods (or altogether) as that would be a noteworthy event. What are you trying to glean from such information if you don't mind me asking?
Best wishes, niekell.