Find connector.php inside the filemanager plugin folder, open it in an editor and add these lines to the roots array below accessControl:

'attributes' => array(                
   array(
             'pattern' => '/.tmb/',
             'read' => false,
             'write' => false,
             'hidden' => true,
             'locked' => false
            )

)

If you want more than one type of files to stop showing up in the filemanager, you can do this:

'attributes' => array(                
   array(
             'pattern' => '/.tmb/',
             'read' => false,
             'write' => false,
             'hidden' => true,
             'locked' => false
            ),
   array(
             'pattern' => '/.quarantine/',
             'read' => false,
             'write' => false,
             'hidden' => true,
             'locked' => false
            )
)

The whole $opts will look like this:

$opts = array(
    'roots' => array(
        array(
            'driver'        => 'LocalFileSystem',   // driver for accessing file system (REQUIRED)
            'path'          => $abspath['path'],         // path to files (REQUIRED)
            'URL'           => $abspath['URL'],  //$plugin_arr, // URL to files (REQUIRED)
            'accessControl' => 'access',             // disable and hide dot starting files (OPTIONAL)
            'attributes' => array(                
               array(
                         'pattern' => '/.tmb/',
                         'read' => false,
                         'write' => false,
                         'hidden' => true,
                         'locked' => false
                        )

            )
        ),

    )
);

Any folder path you write, all its subfolders will show up in the folders list. But make sure you copy the path from the server exactly, the paths are usually like this:
/public_html/www/mysite/wp-content/uploads/