Copying whole directory trees on a running system is not easy. I would use tar instead of cp. On source machine (note option -l, a.k.a. --one-file-system, to avoid recursion): tar -clf - / | tar -xf - -C /mnt/portable and on target machine: tar -cf - -C /mnt/portable * | tar -xf - -C /mnt/target Risto