Those appear to be subfolders, but they're not. They're feature datasets, which have
a very specific purpose. Using them as folders introduces a number of limitations and
unintended consequences, and is therefore not recommended. The impact is less
severe in FGDB than in ArcSDE, but it can introduce a bad habit that will be difficult
to break. Creating different FGDBs for different study areas is IMHO a much better
practice.
- V