If you are making your custom module in magento and if you unable to use default magento file upload then you can use magento custom file uploading code to upload file.
// If you want to upload files under media folder
$absolute_path = Mage::getBaseDir('media') . DS ;
$relative_path = Mage::getBaseUrl(Mage_Core_Model_Store::URL_TYPE_MEDIA);
// File Upload
$files = $_FILES['file_upload']['name'];
if(isset($files) && $files != '')
{
try
{
if(file_exists($absolute_path.DS.$files))
{
$var = rand(0,99);
$files = $var.'_'.$files;
}
// Starting upload
$uploader = new Varien_File_Uploader('file_upload');
// Any extention would work
$uploader->setAllowedExtensions(array('jpg','jpeg','gif','png'));
$uploader->setAllowRenameFiles(false);
//false -> get the file directly in the specified folder
//true -> get the file in the product like folders /media/catalog/product/file.gif
$uploader->setFilesDispersion(false);
//We set media as the upload dir
$uploader->save($absolute_path, $files);
}
catch(Exception $e)
{
Mage::getSingleton('adminhtml/session')->addError($e->getMessage());
}
// Your uploaded file Url will be
echo $file_url = $relative_path.$files;
}