I have following structure of my project
/system
/applications
/cache
/core
/helpers
/hook
/language
/libraries
/logs
/third_party
/admin-p
if your root folder for project is not root of domain i.e. your website is subdirectory of a domain http://localhost/myproject
then you need an additional line in your .htaccess file that is RewriteBase
RewriteEngine On
RewriteBase /myproject
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ index.php/$1 [L]
Also make sure, your config.php is configured as
$config['base_url'] = 'http://localhost/myproject/';
$config['index_page'] = '';
And mod_rewrite is enable in apache's config file.