Navigate to your project's or project template's Files page. Click on Internal Files or Public Files, this will show you the respective documents. Click on Actions -> Delete adjacent to the file you'd like to remove.
If your file doesn't disappear immediately, please try refreshing the page.
Will deleting files from a Project Template delete them from the File Library?
Absolutely not! For organizations that are using the File Library module, when deleting files from a Project Template, if the files are stored within your File Library they will still exist there and will not be removed.