Instruction :- Copy and save this code file in root folder of Magento and run it;
exp :- http://yoursite/deletecat.php
<?php error_reporting(E_ALL | E_STRICT); $mageFilename = 'app/Mage.php'; require_once $mageFilename; Mage::setIsDeveloperMode(true); ini_set('display_errors', 1); ini_set('max_execution_time', 1800); umask(0); Mage::app()->setCurrentStore(Mage_Core_Model_App::ADMIN_STORE_ID); foreach(Mage::getModel('catalog/category') ->getCollection() ->addFieldToFilter('entity_id', array('gt' => 2)) as $cat) { $cat->delete(); } ?>