Group and send all files to filetype folder
Avoid os.system() by all means. It wastes resources by creating 2 processes per invocation, and is vulnerable to various attacks (at least spell out full paths to the mkdir and mv utilities).

os.mkdir() provide all necessary functionality (don't forget to catch OSError). A combination of os.link() and os.unlink() emulates mv (they are only available on Unix - but you are calling mv anyway).