There no easy way to do this.
You could enable XML logging, list the contents of the directory, generate set of mv commands only for the files and run the command set.
See documentation:
https://winscp.net/eng/docs/guide_interpreting_xml_log

Hi,

I have a directory called /Root/ and I need to copy only the files that exist in /Root/ to /Root/SubDir

When i execute "mv *.* /SubDir/ it fails telling me I cannot copy the file SubDir to /Subdir/Subdir

Is it possible to only moves the files in the current directory, or will it always copy the directories whenever i provide the wildcard?