> are all into directories and sub-directories - and I
> want to maintain the directory structure. 

Options -> Build -> Local Structure Type

> The second requirement is that I do not want httrack
> to mess up the URL in the downloaded pages. eg: in
> one of my tries - it started downloading php pages -
> and renaming them. As a result the links to those
> php pages in the downloaded pages were all messed

You can't get server side pages (php, jsp, asp...) from the front of a server,
you only get html.  Httrack will download all the pages and rename them to
.html and change the links to match.