how to remove wrapper for boxes?
I have not tried Boxes myself, but looking at its code, it looks like they use a theme function to produce the markup for the boxes.

If you implement theme_boxes_box (found in boxes.admin.inc) in your own theme/module you can just copy the code from it and remove the markup you don't want.

/**
 * Overrides theme_boxes_box().
 */
function MYMODULE_boxes_box($variables) {
  $block = $variables['block'];

  $empty = '';

  // Box is empty
  if ((empty($block['title']) || ($block['title'] == '&lt;none&gt;') ) &amp;&amp; empty($block['content'])) {

    // add a class to mark the box as empty
    $empty = ' box-empty';

    // show something if the block is empty but the user has the permission to edit it
    if (boxes_access_edit()) {
      $block['content'] = t('This box appears empty when displayed on this page. This is simply placeholder text.');
    }
    else {
      return;
    }
  }

  $output = "&lt;div id='boxes-box-" . $block['delta'] . "' class='boxes-box" . (!empty($block['editing']) ? ' boxes-box-editing' : '') . $empty . "'&gt;";
  $output .= '&lt;div class="boxes-box-content"&gt;' . $block['content'] . '&lt;/div&gt;';
  if (!empty($block['controls'])) {
    $output .= '&lt;div class="boxes-box-controls"&gt;';
    $output .= $block['controls'];
    $output .= '&lt;/div&gt;';
  }
  if (!empty($block['editing'])) {
    $output .= '&lt;div class="box-editor"&gt;' . drupal_render($block['editing']) . '&lt;/div&gt;';
  }
  $output .= '&lt;/div&gt;';
  return $output;
}