> i was trying to get a single file from this URL
> (http://purl.pt/728/) but since the server redirects the
> response to the file instead of sending to the URL of the
> pdf httrack names it as index.html since it has no name 
for it.
> The only thing missing is the right extension although it
> might not be easy. 
> If you could do something about it, it would be great.

This might help:
Set Options / Spider / Check document type: If Unknown