WordPress Rewrite Rules for Custom Post Type and Taxonomy

Hope this can solve your problem

function my_custom_post_type() {
$labels = array(
    'name' => _x('Projects', 'post type general name'),
    'singular_name' => _x('Project', 'post type singular name'),
    'add_new' => _x('Add New', 'project item'),
    'add_new_item' => __('Add New Project'),
    'edit_item' => __('Edit Project'),
    'new_item' => __('New Project'),
    'view_item' => __('View Project'),
    'search_items' => __('Search Projects'),
    'not_found' =>  __('Nothing found'),
    'not_found_in_trash' => __('Nothing found in Trash'),
    'parent_item_colon' => '',
    'menu_name' => 'Projects' 
);

$args = array(
    'labels' => $labels,
    'public' => true,
    'publicly_queryable' => true,
        'hierarchical' => false,
        'has_archive' => true,
    'rewrite' => array('slug'=>'work', 'with_front'=>false),
    'show_ui' => true,
    '_builtin' => false, // It's a custom post type, not built in!
    'capability_type' => 'post',
        'query_var' => true, // This goes to the WP_Query schema
    'menu_position' => null,
    'supports' => array('title','editor','thumbnail', 'comments', 'author', 'excerpt')
);

register_post_type( 'work' , $args );

}
function my_custom_taxonomies() {

    $labels = array(
        'name' => __( 'Taxonomy', 'taxonomy general name' ),
        'singular_name' => __( 'Taxonomy', 'taxonomy singular name' ),
        'search_items' =>  __( 'Search Taxonomy' ),
        'all_items' => __( 'All Taxonomy' ),
        'parent_item' => __( 'Parent Taxonomy' ),
        'parent_item_colon' => __( 'Parent Taxonomy:' ),
        'edit_item' => __( 'Edit Taxonomy' ), 
        'update_item' => __( 'Update Taxonomy' ),
        'add_new_item' => __( 'Add New Taxonomy' ),
        'new_item_name' => __( 'New Taxonomy Name' ),
        'menu_name' => __( 'Taxonomy' ),
    );  

    register_taxonomy( 'taxonomy', array('work'), array (
                    'labels' => $labels,
                    'hierarchical' =>false,
                    'show_ui' => true,
                    'rewrite' => array( 'slug' => 'work/taxonomy'),
                    'query_var' => true,
                    'show_in_nav_menus' => true,
                    'public' => true,
            ));
}

add_action('init', 'my_custom_post_type', 0);
add_action('init', 'my_custom_taxonomies', 10);

what you need to create is archive-work.php (your post type archive)
and taxonomy.php which will use to show your custom taxonomy archive.