To transfer data from local system to Arduino Yun you have to establish the SSH connection between both system by using PuTTY software. Open the PuTTY configuration Window, Enter the IP address or username of the Arduino Yun in Hostname section. Select connection type to SSH.
Then click to connect and enter the username and password when prompted.
Now you successfully connection to Arduino Yun and perform transfer data through command line interface.
https://puttykeyinfo.com/ ...is not the official PuTTY site. What is "Putty Key Info"?
I know it, but here I find the whole procedure to download and transfer file between system, and other various aspect related to PuTTY.