So, as you have cleared, you want to delete file(s) located in client side after you upload the file(s) to the server.
As it is clear from your statement that this application will be run from a controlled environment. So, you need some security access permission to delete the files from the folder.
In Javascrip, try this..
<script type="text/javascript">
var fso = new ActiveXObject('Scripting.FileSystemObject');
fso.DeleteFile("C:\\Temp\\customefolder\\file.txt, true);
fso = null;
</script>
hope this helps.
cheers