$productObj = Mage::getModel('catalog/product')->load($product->getId());
$productObj->setData('filter_category','51,52');
$productObj->save();

$attrCode = 'your_attribute';
$sourceModel = Mage::getModel('catalog/product')->getResource()
    ->getAttribute($attrCode)->getSource();
$valuesText = explode(',', 'red,green,blue');
$valuesIds = array_map(array($sourceModel, 'getOptionId'), $valuesText);
$product->setData($attrCode, $valuesIds);
$product->getResource()->saveAttribute($product, $attrCode);

public function setFilterCategoryBeforeSave(Varien_Event_Observer $observer)
{
    $observer->getProduct()->setData('filter_category','51,52');
}

$collection = $this->getCollection()
            ->addAttributeToSelect('*')
            ->addAttributeToFilter('visibility', $visibility)
            ->addAttributeToFilter('status', Mage_Catalog_Model_Product_Status::STATUS_ENABLED)
            ->addAttributeToFilter($attribute,array('finset'=>array_search($selection,$valueId)))
            ->setPageSize($limit)
            ->load();
        Mage::getSingleton('cataloginventory/stock')->addInStockFilterToCollection($collection);