Hello,
for what I undertand, you need to remove user specific permissions to folders and subfolders, and then set groups instead.
You can remove single user permissions from folders and subfolders via command line, or if you prefer you can also reset the ACLs to default for all the folders/subfolders and then re-set up them from scratch.
What is the operating system version of this file server?
Please feel free to contact me to discuss the details further.
Look forward to hearing from you soon.
Best regards,
Davide - MCP, VCP