Do I need to delete uploaded files if I only want to parse them
According to the docs for file_save_upload() the file will be registered as a temporary file, so that it will be deleted anyway, assuming you have cron running on a regular basis.


  "The file will be added to the {file_managed} table as a temporary file. Temporary files are periodically cleaned. To make the file a permanent file, assign the status and use file_save() to save the changes."