Since you posted this in the
Servlets forum I assume that this should be done in a web app. HTML forms can upload multiple files to a servlet container, but you would need to select the files one by one. There's no way to select a directory, or multiple files in the same file selection dialog.
If you want to select several files at the same time you need to use an
applet, or a similar technology.
The file handling in the servlet container can be done using a library like Apache Commons FileUpload.