As uSlackr already mentioned there is a big different depending on whether your server is a member (standalone) server or in a domain with permissions only set to domain accounts.
If you are in a domain, you don't have to do anything, because the DACLs on your files have ACE with Domain SIDs in them, they are still valid after you installed a new OS.
If you have a standalone server, it is more complicated. Even if you create users and groups with the same names, the ACEs will no longer work. Copying files including they DACL information will not help you because the DACL on the source files are broken.
If you only have a handful of different permissions at the top folder levels, it may be easiest to clear all permissions and set them new from scratch using a script which then also acts as a documentation for your permission policies.
If you have lots of different users/groups with many different permissions on different folder/files, you have to create a program or PowerShell script to replace the old ACEs with new ones. You would use a mapping table between the old SIDs and the new ones and then
replace all ACEs on all files/folders recursively. I can image there are already tools out there that do this, but I don't know of any of hand.