Removing index.php in CodeIgniter just works for t

This is the code that I put in my .htaccess

RewriteEngine on
RewriteCond $1 !^(index\.php|images|robots\.txt)
RewriteRule ^(.*)$ /index.php/$1 [L]

it works just fine if I go the default controller

$route['default_controller'] = "atk_c/login";

I just input localhost/timetracker and it will automatically goes to the login page. but when I need to go to another page besides that page. It displays the error "Not Found".

Example:

<a href="<?php echo base_url('atk_c/register'); ?>"> Not yet registered? Click here!</a>

This worked for me:

Make sure you remove index.php in config.php like this:

$config['index_page'] = '';

And this is my .htaccess

<IfModule mod_rewrite.c>
    RewriteEngine On
    RewriteBase /

    #Removes access to the system folder by users.
    #Additionally this will allow you to create a System.php controller,
    #previously this would not have been possible.
    #'system' can be replaced if you have renamed your system folder.
    RewriteCond %{REQUEST_URI} ^system.*
    RewriteRule ^(.*)$ /index.php?/$1 [L]

    #When your application folder isn't in the system folder
    #This snippet prevents user access to the application folder
    #Submitted by: Fabdrol
    #Rename 'application' to your applications folder name.
    RewriteCond %{REQUEST_URI} ^application.*
    RewriteRule ^(.*)$ /index.php?/$1 [L]

    #Checks to see if the user is attempting to access a valid file,
    #such as an image or css document, if this isn't true it sends the
    #request to index.php
    RewriteCond %{REQUEST_FILENAME} !-f
    RewriteCond %{REQUEST_FILENAME} !-d
    RewriteRule ^(.*)$ index.php?/$1 [L]
</IfModule>

<IfModule !mod_rewrite.c>
    # If we don't have mod_rewrite installed, all 404's
    # can be sent to index.php, and everything works as normal.
    # Submitted by: ElliotHaughin

    ErrorDocument 404 /index.php
</IfModule>