So if you want them get added to Valid.

if (!filenameRec.next()){ // We are checking here, if recoed doesn't exists

      filenameRec.file_name=filenameArr[i];

      filenameRec.active='true';

      id = filenameRec.insert();

      //valid.push(filenameArr[i]); // valid will have sn.te - Comment this

  }

else

{

          valid.push(filenameArr[i]); // Add values which already exists to Valid variable

}