Unless your program is really big, don’t organize the modules in a hierarchy. Why not? Because although computers are good at hierarchy, people aren’t. People are good at meaningful names. If you choose good names you can easily handle 150 modules in a flat name space.
I felt like [a flat name space] lacked organization.
Hierarchical organization is not an end in itself. To justify splitting modules up into a hierarchy, you need a reason. Good reasons tend to have to do with information hiding or reuse. When you bring in information hiding, you are halfway to a library design, and when you are talking about reuse, you are effectively building a library. To morph a big program into “smaller program plus library” is a good strategy for software evolution, but it looks like you’re just starting, and your program isn’t yet big enough to evolve that way.
These issues are largely independent of the programming language you are using. I recommend reading some of David Parnas’s work on product lines and program families, and also Matthias Blume’s underappreciated paper Hierarchical Modularity. These works will give you some more concrete ideas about when hierarchy starts to serve a purpose.