If your goal is to prevent using dir then you'd have to disable the command prompt and powershell (which would likewise have a dir alias) access to users. This can be done via GPO. Assuming you just want to modify the ntfs permissions for C:\Windows , default NTFS permissions allow for all users to read and execute and modifying it may have unintended consequences. You can modify the ntfs permissions by right clicking the folder, selecting properties, and then the security tab and clicking modify/edit assuming you have administrator privileges.
Remove or deny the NTFS permission called "List Folder Contents" https://www.ntfs.com/ntfs-permissions-file-advanced.htm
If you can't change then you need to take ownership with an admin account. (local/domain admin)
If your goal is to prevent using dir then you'd have to disable the command prompt and powershell (which would likewise have a dir alias) access to users. This can be done via GPO. Assuming you just want to modify the ntfs permissions for C:\Windows , default NTFS permissions allow for all users to read and execute and modifying it may have unintended consequences. You can modify the ntfs permissions by right clicking the folder, selecting properties, and then the security tab and clicking modify/edit assuming you have administrator privileges.