You cannot do anything other than append items to a FormData object. See the Spec. It would be better if you use a dictionary/object to store all the values you want to add/modify before you actually construct the object.
var data = {};
jQuery.each($('#file')[0].files, function(i, file) {
data['file-'+i] = file;
});
//modify the object however you want to here
var formData = new FormData();
for (var key in data) {
formData.append(key, data[key]);
}