Queue up each directory you wish to transfer by right clicking on it, queue as path. Or use the command line: corecmd.exe -s -site siteprofile -u c:\path\ -p /remote-path/ -log c:\logs\logfile.txt or corecmd.exe -s -recurse -site siteprofile -u c:\path\* -p /remote-path/ -log c:\logs\logfile.txt