If you need to create a folder in SharePoint2010 root folder and set permission to it, here is piece of code that does it. In the script, I have created a folder called Temp in Logs folder under SharePoint2010 root and then I grant read/write access to the Windows group WSS_WPG and full access to the group WSS_ADMIN_WPG for that folder.

$Folder=New-Item "C:\Program Files\Common Files\Microsoft Shared\Web Server Extensions\14\LOGS\temp" -Type Directory -force
$acl = Get-Acl $Folder
##The following line has been commented out , if you like to break the permission inheritance from the parent floder , uncommented the code.
#$acl.SetAccessRuleProtection($True, $False)
$rule = New-Object System.Security.AccessControl.FileSystemAccessRule("WSS_ADMIN_WPG","FullControl", "ContainerInherit, ObjectInherit", "None", "Allow")
$acl.AddAccessRule($rule)
$rule = New-Object System.Security.AccessControl.FileSystemAccessRule("WSS_WPG","Modify", "ContainerInherit, ObjectInherit", "None", "Allow") 
$acl.AddAccessRule($rule)
Set-Acl $Folder $acl

References:

http://technet.microsoft.com/en-us/library/ff730951.aspx

http://msdn.microsoft.com/en-us/library/tbsb79h3.aspx

http://blogs.technet.com/b/josebda/archive/2010/11/12/how-to-handle-ntfs-folder-permissions-security-descriptors-and-acls-in-powershell.aspx

http://chrisfederico.wordpress.com/2008/02/01/setting-acl-on-a-file-or-directory-in-powershell/