w60houes I’m afraid you did something wrong. Tonfotos does not create this directory structure unless you ask it directly to do that. All you needed to do is to add this folder to the Library locations, and it will scan it as is. However, I assume once you plugged it in, there was popus asking to import (meaning copy) your files to your main library (which happens to be the same drive), and that started copying process. This function is designed to import files from phones and cameras, but for some reason Windows does not makes too much distiction sometimes between camera and regular USB hard drive.
I would suggest you to stop this process (by closing down the applicaiton). And then next time this popup will appear, tell it to never popup again for this drive.
Then you probably will want to delete those newly created folders. But before doing that I would suggest to wait for scanning to finish, and then you will be able to see which files are duplicates and which not.