I have not used it personally, but have had BlueHarvest recommended to me for this...
http://www.zeroonetwenty.com/blueharvest4/
From the site:
The easiest way to keep your disks and file servers clean of Mac “dust”. BlueHarvest automatically removes DS_Store and ._ AppleDouble files (resource forks) from your USB keys, SD cards and file servers, etc. BlueHarvest removes these items as they’re created so you’ll always be “dust” free.