If you are using onchange="{! c.handleFilesChange }" on the lightning:input component, you can get the list of files by using the following command: event.getSource().get("v.files"), according to the docs.
I have tried it myself (on v40) and it is working.
..helper.js:
handleFilesChange : function(component, event)
{
var uploadFile = event.getSource().get("v.files")[0];
}