Prevent Visitor Accessed Direct Controller & Fix Main Url on Code Igniter config base url not set

MY_Config.php

<?php
/**
 * Hackie of CI 3 Core URL Fix Sanitized
 * Automation detect base url
 * @pentagonal
 */
if (!class_exists('CI_Config')) {
    return;
}

class MY_Config extends CI_Config
{
    /**
     * Constructor
     *
     * Override Config Core to Auto Detection URL if Config URL does not set
     */
    public function __construct()
    {
        // CI use refference to allow arguments take override nested
        $this->config =& get_config();

        // Set the base_url automatically if none was provided
        if (empty($this->config['base_url']) || trim($this->config['base_url']) == '') {
            /**
             * Auto Detection URL on Code Igniter
             */
            if (isset($_SERVER['HTTP_HOST'])) {
                $base_url = $this->portUrlMessDetector($_SERVER['HTTP_HOST']);
            } elseif (isset($_SERVER['SERVER_NAME'])) {
                $base_url = $this->portUrlMessDetector($_SERVER['HTTP_HOST']);
            } elseif (isset($_SERVER['SERVER_ADDR'])) {
                // this is IPV 6 ipv 6 accessed by http(s)://[11:22:33:44]/
                if (strpos($_SERVER['SERVER_ADDR'], ':') !== false) {
                    $base_url = $this->portUrlMessDetector('['.$_SERVER['SERVER_ADDR'].']');
                } else {
                    $base_url = $this->portUrlMessDetector($_SERVER['SERVER_ADDR']);
                }
            } else {
                // default host , but it will be almost impossible, if server config has not wrong!
                $base_url = 'http://localhost/';
            }

            $this->set_item('base_url', $base_url);
        }
        // do it like core , send log into system
        log_message('info', 'Config Class Initialized');
    }

    /**
     * Fixing the server address & URL
     *
     * @param  string $server_addr url
     * @return string base URL
     */
    protected function portUrlMessDetector($server_addr)
    {
        /**
         * Base on Different port not 80 / 443
         */
        if (isset($_SERVER['SERVER_PORT'])) {
            $server_addr .= $_SERVER['SERVER_PORT'] != 80 && $_SERVER['SERVER_PORT'] != 443
                ? ':'.$_SERVER['SERVER_PORT']
                : '';
        }

        $base_url = (is_https() ? 'https' : 'http').'://'. $server_addr
            . substr($_SERVER['SCRIPT_NAME'], 0, strpos($_SERVER['SCRIPT_NAME'], basename($_SERVER['SCRIPT_FILENAME'])));
        return $base_url;
    }
}

MY_Router.php

<?php
/**
 * Hackie of CI 3 Core URL Fixed Sanitizer
 * Prevent direct access to Uri Controller
 * @pentagonal
 */
if (!class_exists('CI_Router')) {
    return;
}

class MY_Router extends CI_Router
{
    /**
     * Parse Routes
     *
     * Matches any routes that may exist in the config/routes.php file
     * against the URI to determine if the class/method need to be remapped.
     *
     * @return  void
     */
    protected function _parse_routes()
    {
        // Turn the segment array into a URI string
        $uri = implode('/', $this->uri->segments);

        // Get HTTP verb
        $http_verb = isset($_SERVER['REQUEST_METHOD']) ? strtolower($_SERVER['REQUEST_METHOD']) : 'cli';

        // Loop through the route array looking for wildcards
        foreach ($this->routes as $key => $val) {
            // Check if route format is using HTTP verbs
            if (is_array($val)) {
                $val = array_change_key_case($val, CASE_LOWER);
                if (isset($val[$http_verb])) {
                    $val = $val[$http_verb];
                } else {
                    continue;
                }
            }

            // Convert wildcards to RegEx
            $key = str_replace(array(':any', ':num'), array('[^/]+', '[0-9]+'), $key);

            // Does the RegEx match?
            if (preg_match('#^'.$key.'$#', $uri, $matches)) {
                // Are we using callbacks to process back-references?
                if ( ! is_string($val) && is_callable($val)) {
                    // Remove the original string from the matches array.
                    array_shift($matches);
                    // Execute the callback using the values in matches as its parameters.
                    $val = call_user_func_array($val, $matches);
                } elseif (strpos($val, '$') !== false && strpos($key, '(') !== false) {
                    // Are we using the default routing method for back-references?
                    $val = preg_replace('#^'.$key.'$#', $val, $uri);
                }

                $this->_set_request(explode('/', $val));
                return;
            }
        }

        /**
         * We Must Comment this ,
         * because it will be allow visitor access by direct Controller CLASS!
         * if you have Controller Wellcome 
         * and user access
         * http://example.com/index.php/Wellcome
         * it will be same as http://example.com/index.php/(<url to controller route>)
         */
        /*
        // If we got this far it means we didn't encounter a
        // matching route so we'll set the site default route
        $this->_set_request(array_values($this->uri->segments));
        */
    }
}

where should I put these files? will it prevent direct access all controller's method except ajax call? Little help required.
Thanks in advance