Part of my daily work involves transferring of data from my system to client system using MSTSC, is it possible to automate this transfer or is there any command line that i can use instead of connecting to the Jumpbox and then manually moving the files.
There is no command line switch or Remote Desktop Services API to let you to access the remote session.
You can write a file server (e.g. FTP) or a virtual channel to transfer the files.