There are three main methods for organizing data files: sequential, direct, and indexed. Sequential organization stores records in order by a key field, requiring reading all prior records to access a specific one. Direct organization allows random access via a record key and a formula to derive the disk address. Indexed organization stores records sequentially but also has an index containing the record key and associated address for direct access. Data can be processed via batch or transaction processing. Batch processing collects transactions into batches to update the master file periodically, while transaction processing handles each transaction immediately as it occurs.