Example method to remove simple $form['#prefix'] and $form['#suffix'] elements from rendered markup in a Drupal 6 page preprocess function using SimpleXMLElement.

gistfile1.php

/**
 * Page preprocess.
 */
function phptemplate_preprocess_page(&$variables) {
  // Return the fully rendered search block, and its SimpleXMLElement equivalent.
  $block = theme('block', (object) module_invoke('google_appliance', 'block', 'view', 'google_search'));
  $block_xml = new SimpleXMLElement($block);

  // Parse out $form['#prefix'] and $form['#suffix']
  $prefix = $block_xml->xpath('//form/preceding-sibling::*[1]');
  $suffix = $block_xml->xpath('//form/following-sibling::*[1]');

  // Replace relevant XML bits in the rendered markup.
  $to_be_replaced = array($prefix[0]->asXML(), $suffix[0]->asXML());
  $replacements = array('', '');
  $block = str_replace($to_be_replaced, $replacements, $block);

  // Assign the final, processed block HTML.
  $variables['search_box'] = $block;
}