Remove custom taxonomy base from URL

Depending on how you are registering your custom post types, you can simply set the rewrite rules for it like so:

$args = array(
        'description' => 'Photograph Post Type',
        'label' => __('Photographs'),
        'public' => true,
        'rewrite' => array( 'slug' => 'photograph'),
);

register_post_type( 'photograph' , $args );

If (for some bizarre reason) you don’t have access to modify the way in which your custom post types are being registered, try setting the “category base” to “.” within the Permalinks menu in your admin panel, and make sure that your permalink structure is set to /%category%/%postname%/. That’s worked for me in the past.