Judging by the application's online documentation, I don't think that is possible as WinToUSB also clones the third-party tools installed on your Windows. However, I recommend contacting the developers using this email address: support@easyuefi.com
and asking them directly if there is any way for you to select which files and programs get cloned to the USB memory stick.
Alternatively, you could try installing a secondary Windows on a different partition, setting up the applications that you need, then cloning that operating system instead of your main one.