$args = array(
            'labels'                     => $labels,
            'hierarchical'               => true,
            'public'                     => true,
            'show_ui'                    => true,
            'show_admin_column'          => true,
            'show_in_nav_menus'          => true,
            'show_tagcloud'              => true,
            'rewrite'                    => array( 'slug' => 'filter', 'with_front' => false ),
        );
        register_taxonomy( 'service', 'filter', $args );

/* Register CPT
*/
function wpse_138987_post_type_filter() {
 register_post_type('filter', array(
    'labels' => array(
        'name' => 'Filter',
        'all_items' => 'All Posts'
    ),
    'public' => true
 ));
}
add_action('init', 'wpse_138987_post_type_filter');

// register taxonomy
function wpse_138987_taxonomy_service() {
 register_taxonomy('service', array('filter'), array(
    'labels' => array(
        'name' => 'Service'
    ),
    'hierarchical'               => true,
    'public'                     => true,
    'show_ui'                    => true,
    'show_admin_column'          => true,
    'show_in_nav_menus'          => true,
    'show_tagcloud'              => true,
    'rewrite' => array('slug' => 'filter')
));
}
add_action('init', 'wpse_138987_taxonomy_service');


/*
 * Replace Taxonomy slug with Post Type slug in url
*/
function taxonomy_slug_rewrite($wp_rewrite) {
  $rules = array();
  // get all custom taxonomies
  $taxonomies = get_taxonomies(array('_builtin' => false), 'objects');
  // get all custom post types
  $post_types = get_post_types(array('public' => true, '_builtin' => false), 'objects');

  foreach ($post_types as $post_type) {
    foreach ($taxonomies as $taxonomy) {

        // go through all post types which this taxonomy is assigned to
        foreach ($taxonomy->object_type as $object_type) {

            // check if taxonomy is registered for this custom type
            if ($object_type == $post_type->rewrite['slug']) {

                // get category objects
                $terms = get_categories(array('type' => $object_type, 'taxonomy' => $taxonomy->name, 'hide_empty' => 0));

                // make rules
                foreach ($terms as $term) {
                    $rules[$object_type . '/' . $term->slug . '/?$'] = 'index.php?' . $term->taxonomy . '=' . $term->slug;
                }
            }
        }
    }
}
// merge with global rules
$wp_rewrite->rules = $rules + $wp_rewrite->rules;
}
add_filter('generate_rewrite_rules', 'taxonomy_slug_rewrite');

archive-filter.php
 single-filter.php
 taxonomy-service.php

function generate_taxonomy_rewrite_rules( $wp_rewrite ) {
  $rules = array();
  $post_types = get_post_types( array( 'name' => 'portfolio', 'public' => true, '_builtin' => false ), 'objects' );
  $taxonomies = get_taxonomies( array( 'name' => 'services', 'public' => true, '_builtin' => false ), 'objects' );
  foreach ( $post_types as $post_type ) {
    $post_type_name = $post_type->name; // 'developer'
    $post_type_slug = $post_type->rewrite['slug']; // 'developers'
    foreach ( $taxonomies as $taxonomy ) {
      if ( $taxonomy->object_type[0] == $post_type_name ) {
        $terms = get_categories( array( 'type' => $post_type_name, 'taxonomy' => $taxonomy->name, 'hide_empty' => 0 ) );
        foreach ( $terms as $term ) {
          $rules[$post_type_slug . '/' . $term->slug . '/?$'] = 'index.php?' . $term->taxonomy . '=' . $term->slug;
          $rules[$post_type_slug . '/' . $term->slug . '/page/?([0-9]{1,})/?$'] = 'index.php?' . $term->taxonomy . '=' . $term->slug . '&paged=' . $wp_rewrite->preg_index( 1 );
        }
      }
    }
  }
  $wp_rewrite->rules = $rules + $wp_rewrite->rules;
}
add_action('generate_rewrite_rules', 'generate_taxonomy_rewrite_rules');

function generate_taxonomy_rewrite_rules( $wp_rewrite ) {

$rules = array();

$post_types = get_post_types( array('public' => true, '_builtin' => false ), 'objects' );
$taxonomies = get_taxonomies( array('public' => true, '_builtin' => false ), 'objects' );

foreach ( $post_types as $post_type ) {
    $post_type_name = $post_type->name;
    $post_type_slug = $post_type->rewrite['slug'];

    foreach ( $taxonomies as $taxonomy ) {//echo 'DDDDD'; print_r($taxonomy);
        if ( $taxonomy->object_type[0] == $post_type_name ) {
            $terms = get_categories( array( 'type' => $post_type_name, 'taxonomy' => $taxonomy->name, 'hide_empty' => 0 ) );
            //print_r($terms);
            foreach ( $terms as $term ) {
                $rules[ $taxonomy->name.'/'. $term->slug . '/?$'] = 'index.php?' . $term->taxonomy . '=' . $term->slug;
                $rules[ $taxonomy->name.'/'. $term->slug . '/page/?([0-9]{1,})/?$'] = 'index.php?'.'type='.$post_type_name."&" . $term->taxonomy . '=' . $term->slug . '&paged=' . $wp_rewrite->preg_index( 1 );

            }
        }
    }
}

$wp_rewrite->rules = $rules + $wp_rewrite->rules;

}

add_action('generate_rewrite_rules', 'generate_taxonomy_rewrite_rules');