I am not familiar with jQuery File Tree but I believe that the key to your issue lies inside the loops.
The only thing you need to do is create a blacklist, an array with the name of the folders/files you dont want to show.
$blacklist = array('namefile1', 'namefolder1', 'namefile2');
And then implement a check inside the loop, so that it skips the name if the file/folder name matches one that is inside the blacklist (case sensitive).
foreach( $files as $file )
{
if (in_array($file, $blacklist))
continue;
.... the rest of the code ...
.... goes here ..............
}
That is basically what you need to do. You could also use regular expressions and the preg_match function, to make it more flexible..