You need to put your WinSCP commands into separate script file.
Please read guide to scripting:
https://winscp.net/eng/docs/guide_automation

I'm trying to write a batch script that transfers files using secureFTP with the WinSCP application.

The script runs and authenticates but seems to stop once the active session starts and leaves the command window open at winscp>

it doesn't put (transfer) my file.

Can anyone help?

Here is my batch script:

cd c:\
cd Program Files (x86)\WinSCP
winscp username:password@secureftp.mycompany.com
cd myTestDirectory
lcd c:\
put test.txt
exit

It seems to stop on cd myTestDirectory. When I run my batch file it just leaves the command console open at winscp>
It definitely shows that it authenticated correctly.

Thanks for any help.