The Advanced Uploader tool can upload multiple files at once and keep a file structure intact.
1) From the User Profile menu, choose Advanced Uploader.
2) Click the Continue button*.
*You might see a window from Java asking for permission to run the Advanced Uploader application. Click Run.
3) The tool will open as a separate application in its own window called Bulk Upload Tool.
4) Click Select a folder on your local drive
5) Select the folder to upload.
When finished, you can upload another folder by clicking Add another folder.