can I customize the Extract/Format Operation Flow or Format Payments in R12

We are  now be generating our own cheques to be sent to a third party for printing. There is limited seeded functionaliity within Payments for renaming our outgoing files so we are looking for a custom solution. Is there a way to add additional custom steps to the Extract and format Operation flow. Specifically we are looking at creating a unix shell that we can integrate into the seeded payment process - basically an additional custom step that would run at the end of Format Payment Instructions. The shell would take the payment output file and renames it in accordance