I am uploading files using servlet my little code is much like this:

ServletFileUpload servletFileUpload = new ServletFileUpload(new DiskFileItemFactory());

try {
    fileItemsList = servletFileUpload.parseRequest(request);
} catch (FileUploadException ex) {
    Logger.getLogger(iThink.class.getName()).log(Level.SEVERE, null, ex);

String optionalFileName = "";
FileItem fileItem = null;

Iterator it = fileItemsList.iterator();

The file is submitted to apache directory (webappsmysiteuploadsabd.zip). Uploading is working fine but I wish to remove it.

Because you already got a listing of FileItem objects you can just iterate over that list and call FileItem#delete around the products. Alternatively use File#delete from Java's standard library.