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Should be easy to do; create a temporary directory, hardlink the files there, run the file manager on that directory, then delete the directory and links when it closes.

Something like:

  mkdir "$HOME/.virtualdirs" 2> /dev/null
  tempdir=$(mktemp -d -p "$HOME/.virtualdirs")
  for file in $*; do
    ln "$file" "$tempdir/$(basename $file)"
  done
  thunar "$tempdir" #replace thunar with your file manager
  rm -r "$tempdir"

Ok, now that it works, you just need the other 999.75 hours to make it into a real application ;)
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