How do I remove a file from the FileList

If you want to delete only several of the selected files: you can’t. The File API Working Draft you linked to contains a note:

The HTMLInputElement interface
[HTML5] has a readonly FileList
attribute, […]
[emphasis mine]

Reading a bit of the HTML 5 Working Draft, I came across the Common input element APIs. It appears you can delete the entire file list by setting the value property of the input object to an empty string, like:

document.getElementById('multifile').value = "";

BTW, the article Using files from web applications might also be of interest.