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 readonlyFileList
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.