> When i 
> finished downloading the site ,it only downloads the htm 
> files,there is a programming code(i think it`s php)that 
> makes the files directory invisible or unreachable.
> i wish you understand me.

If the links/files are invisible, httrack won't be able to 
capture them. You may, playing with filters (Options / Scan 
rules) try to catch them by catching the pages where they 
are refferences ; but there are no other solutions, as the 
filestructure behind the site is generally invisible to 
offline browsers or browsers.