Вот пример кода:

public bool SetAcl(string pathname, string userRights, string username, bool inheritSubDirectories)
{
    if (string.IsNullOrEmpty(pathname))
    {
        return false;
    }

    pathname = pathname.TrimEnd('\\');
    var rights = (FileSystemRights)0;
    if (userRights == "R")
    {
        rights = FileSystemRights.ReadAndExecute;
    }
    else if (userRights == "C")
    {
        rights = FileSystemRights.ChangePermissions;
    }
    else if (userRights == "F")
    {
        rights = FileSystemRights.FullControl;
    }

    var accessRule = new FileSystemAccessRule(username, rights,
                                InheritanceFlags.None,
                                PropagationFlags.NoPropagateInherit,
                                AccessControlType.Allow);
    var info = new DirectoryInfo(pathname);
    var security = info.GetAccessControl(AccessControlSections.Access);
    bool result;
    security.ModifyAccessRule(AccessControlModification.Set, accessRule, out result);
    if (!result)
    {
        return false;
    }

    InheritanceFlags iFlags = InheritanceFlags.ObjectInherit;
    if (inheritSubDirectories)
    {
        iFlags = InheritanceFlags.ContainerInherit | InheritanceFlags.ObjectInherit;
    }
    accessRule = new FileSystemAccessRule(username, rights,
                                iFlags,
                                PropagationFlags.InheritOnly,
                                AccessControlType.Allow);

    security.ModifyAccessRule(AccessControlModification.Add, accessRule, out result);
    if (!result)
    {
        return false;
    }

    info.SetAccessControl(security);
    return true;
}

Код основан на материале поста Setting ACE/ACL permissions in .NET 2.0