try this
$productCollection = Mage::getModel('catalog/product')->getCollection()
->addAttributeToFilter('attribute_set_id', 4)
->addAttributeToFilter( 'sku', array( 'in' => array( 'my-sku1', 'my-sku2', 'my-sku3' ) ) )
->addAttributeToFilter('type_id','bundle')
->addFieldToFilter('status', Mage_Catalog_Model_Product_Status::STATUS_ENABLED);
foreach($productCollection as $product)
{
$bundled = Mage::getModel('catalog/product');
$bundled->load($product->getId());
$selectionCollection = $bundled->getTypeInstance(true)->getSelectionsCollection(
$bundled->getTypeInstance(true)->getOptionsIds($bundled), $bundled);
foreach($selectionCollection as $option)
{
$optionModel = Mage::getModel('bundle/option');
$optionModel->setId($option->option_id);
$optionModel->delete();
}
}
hope this help you