The command line utility to copy files and directory trees is:
XCOPY [SOURCE] [DESTINATION]
i.e.
XCOPY C:\...\ParentFolderName D:\DestinationFolder
This will copy all of the files and folders within the source folder to the destination folder.
You can assign your flash drive to a specific drive letter through disk management. This will only help if you're doing this on the same computers over and over.
Disk Management:
Start > Search "computer management" > Enter > Click on Disk Management > Right Click Drive in Question > Assign Letters & Paths > Assign a specific letter.
To compress the files you'll probably need a third party program like WinZip, PKZip or EasyZip with a command line function.
For Winzip:
http://www.winzip.com/prodpagecl.htm
Command Line Utilities accessible via .BAT file:
http://www.memecode.com/docs/winzip.html
In other words your .BAT file might look something like this if you flash drive was locked to F:
winzip32 -min -a -r -es F:\zipfilename.zip %USERPROFILE%\Downloads\Files\ Note: -min = Minimized, -a = Add, -r = Include Subfolders, -es = Super Fast Compression
If i've done that correctly, that should place all of the files located in C:\Users\yourusername\Downloads\Files\ in a zip file named zipfilename.zip located in drive F:
To extract the files at a different computer with the flash drive locked to F:
winzip32 -e -o F:\zipfilename.zip %USERPROFILE%\Downloads\DestinationFolder\ Note: -e = Extract, -o = Overwrite
That should move the files from the zip file on drive F: to a folder called DestinationFolder in C:\Users\yourusername\Downloads