I've the next directory structure:

C:\mywebsites
  \site_1
  \site_2
  \site_n

In 'site_2' I've joomla installed, however, I've other folders with assets, php scripts, etc. within the 'extra' folders, I've scripts that I am frequently calling, the problem comes after i call JURI::base(), it returns the folder where the script file is, instead of 'site_2' which I am expecting.

How do i overcome this straightforward task?

The main directory is determined in JPATH_BASE.

It's occur the index.php within the Joomla front-end as well as in the /administrator using:

define('JPATH_BASE', dirname(__FILE__));

JURI::base() returns the bottom request path.

define('JPATH_BASE', dirname(FILE))

is return the local drive path.. means c:/site_1/site_2/site_3/

JURI::base()

is return the livefolder path... means http://localhost/site_1/site_2/site_3/