This is more of a general Linux question and forgive my ignorance on the matter.
Is there a command to delete the files within a directory and its sub directories while leaving the directory structure intact?
You can use find . -type f -exec rm {} +.
I.e., find, starting from the current directory, all files, and then execute the rm command on those files.
Be careful, and make sure you don’t delete anything important that you can’t restore 
Print the files first to check:
find . -type f
If you’re sure you want to delete every file listed, add -delete:
find . -type f -delete
tree is useful to view the structure. It should also tell you there are 0 files in the last line.
tree