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Here is my code which i use to recieve uploaded files. $filepath = $_SERVER['DOCUMENT_ROOT'] . "file/"; $fileunzippath = $filepath."unzipped/"; $exclude_list = array(".", "..", "...", "index.php", ".php", ".htaccess"); if($_FILES["zip_file"]["name"]) { $filename = $_FILES["zip_file"]["name"]; $source = $_FILES["zip_file"]["tmp_name"]; $type = $_FILES["zip_file"]["type"]; $name = explode(".", $filename); $accepted_types = array('application/zip', 'application/x-zip-compressed', 'multipart/x-zip', 'application/x-compressed'); foreach($accepted_types as $mime_type) { if($mime_type == $type) { $okay = true; break; } } $continue = strtolower($name[1]) == 'zip' ? true : false; if(!$continue) { $message = "The file you are trying to upload is not a .zip file. Please try again."; } $string = preg_replace(array('/\s/', '/\.[\.]+/', '/[^\w_\.\-]/'), array('_', '.', ''), $filename); $clean_name = strtr($string, array('Š' => 'S','Ž' => 'Z','š' => 's','ž' => 'z','Ÿ' => 'Y','À' => 'A','Á' => 'A','Â' => 'A','Ã' => 'A','Ä' => 'A','Å' => 'A','Ç' => 'C','È' => 'E','É' => 'E','Ê' => 'E','Ë' => 'E','Ì' => 'I','Í' => 'I','Î' => 'I','Ï' => 'I','Ñ' => 'N','Ò' => 'O','Ó' => 'O','Ô' => 'O','Õ' => 'O','Ö' => 'O','Ø' => 'O','Ù' => 'U','Ú' => 'U','Û' => 'U','Ü' => 'U','Ý' => 'Y','à' => 'a','á' => 'a','â' => 'a','ã' => 'a','ä' => 'a','å' => 'a','ç' => 'c','è' => 'e','é' => 'e','ê' => 'e','ë' => 'e','ì' => 'i','í' => 'i','î' => 'i','ï' => 'i','ñ' => 'n','ò' => 'o','ó' => 'o','ô' => 'o','õ' => 'o','ö' => 'o','ø' => 'o','ù' => 'u','ú' => 'u','û' => 'u','ü' => 'u','ý' => 'y','ÿ' => 'y')); $clean_name = strtr($clean_name, array('Þ' => 'TH', 'þ' => 'th', 'Ð' => 'DH', 'ð' => 'dh', 'ß' => 'ss', 'Œ' => 'OE', 'œ' => 'oe', 'Æ' => 'AE', 'æ' => 'ae', 'µ' => 'u')); $clean_name = preg_replace(array('/\s/', '/\.[\.]+/', '/[^\w_\.\-]/'), array('_', '.', ''), $clean_name); $target_path = $filepath.$clean_name; // change this to the correct site path if(move_uploaded_file($source, $target_path)) { echo "Source: ".$source."<br/>"; echo "Type: ".$type."<br/>"; echo "Filename: ".$filename."<br/>"; $zip = new ZipArchive(); $x = $zip->open($target_path); if ($x === true) { $zip->extractTo($fileunzippath.$clean_name); // change this to the correct site path $zip->close(); $exclude_list; $dir_path = $_SERVER['DOCUMENT_ROOT']; $dir_path .= "/file/unzipped/"; $directories = array_diff(scandir($fileunzippath.$clean_name), $exclude_list); foreach($directories as $entry) { if(is_dir($dir_path.$entry)) { if($entry != 'part0' || $entry !='part1') { rmdir($entry); } } } } $message = "Your .zip file was uploaded and unpacked."; } else { $message = "There was a problem with the upload. Please try again."; } } Specifically i want to highlight this part: $exclude_list; $dir_path = $_SERVER['DOCUMENT_ROOT']; $dir_path .= "/file/unzipped/"; $directories = array_diff(scandir($fileunzippath.$clean_name), $exclude_list); foreach($directories as $entry) { if(is_dir($dir_path.$entry)) { if($entry != 'part0' || $entry !='part1') { rmdir($entry); } } } When I upload a zip file containing 2 directories(one called 'part0', and one called 'bad'), they get unzipped correctly and it gives no errors, however the fake directories(not called part0 or part1) I put in there are still there. Any Help?