Beginner Question : Managing Folders On the Server

I’m new to server systems.
My mission is to organize the folders on the servers and assign rights to users.
We have 3 servers, they all have Windows Server 2003 R2 as OS. 30+ terminal servers and some PCs.
Our folders look like garbage for now. We have storage system but its folders look like garbage too.
I have enough time to learn and practice.
Is the answer active directory?
Or is it simple as windows security policy. I mean i create a folder. Then i create department folders inside that folder and begin to constrain users from there.
Or may i use a third party software?
As a result, i want to organize our servers’ folders securely. Any help will be appriciated.