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 
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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