For successful Windows boot and logon as well as program work you need the following folders:
– Program Files
– Program Files (x86)
– Boot (if presented on C)
– “bootmgr” file (if presented on C)
You may exclude certain program folders you don’t need from Program Files and Program Files (x86) and folders/files with documents. media etc. from your user account folder (but NOT entire account folder or Users folder, otherwise logon will fail).