Is it possible to restrict user access to files that need read/write permissions?

I am in the process of implementing electronic payments for a company's AP department.  Dynamics GP (Great Plains) needs to create an EFT file that will get sent to the bank.  After it is created, a script is run that sends the TXT file to the
bank and then renames the file extension to SNT.  Users are logged on to the Great Plains server and have their own permission group.
Because the file is sending payment instructions, it is essential that users cannot modify or create a file with fraudulent payment instructions to the bank (incorrect bank account info).
With testing, I was able to save the file from GP to a folder where users cannot read it's contents, however the script cannot send the file to the bank without "read access" (it says not files available).
Any ideas for solutions?  For instance, is it possible to make Great Plains and/or the script file "system" so that it can override the user profile's permissions? 
I was also looking into the ability to hide the folder/files, but it appears users can choose to view hidden files and folders.

I dont think so you can do it that way..

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