Hi Mark,

I have done this with the CloneZilla live CD, it understands many file systems such as NTFS, FAT32, ext2, ext3, HFS etc...This meant I could boot the CD with an external USB drive plugged into a server and image off the NTFS partitions from the server's drives, did some tinkering with the server, decided this wasn't what I had hoped for and so copied back over the images of the partitions...

CloneZilla can copy at different levels, at the drive, volume or partition level and as requested, can only copy used space. HTH.