I have a file structure of nested folders that contains two shapefiles within each. I was to mimic this structure within a geodatabase, where basically each folder would be a feature datasets and the two shapefiles would be feature classes. Is there a way to automate this. My thought would be using the name to group the feature classes into feature datasets.
Feature datasets are not designed as a file managment tool. They are desigined to contain feature classes that have specal related functionality like topology or a network dataset. If you want to organize your data, I suggest creating a serires of file geodatabases as logical containers.