Here is how i solved it. It transferes files from the SD-card to a subfolder in the FTP directory. It cleans up old empty folders as well.
Sub CopyLogToFTP
Dim sourceDirectory = "\SDCard\Dataset0\"
Dim targetDirectory = "\User\SysmacHMI\FTP\"
For Each folder As String In System.IO.Directory.GetDirectories(sourceDirectory)
Dim folderDate = System.IO.Directory.GetCreationTime(folder)
For Each file As String In System.IO.Directory.GetFiles(folder)
Dim fileName = System.IO.Path.GetFileName(file)
Dim fileCreationDate As String = System.IO.File.GetCreationTime(file).ToString("yyMMdd")
Dim datePath As String = System.IO.Path.Combine(targetDirectory, fileCreationDate)
Dim fullPath As String = System.IO.Path.Combine(datePath, fileName)
If System.IO.Directory.Exists(datePath) Then
Else
System.IO.Directory.CreateDirectory(datePath)
End If
If System.IO.File.Exists(fullPath) Then
Else
System.IO.File.Copy(file, fullPath)
End If
System.IO.File.Delete(file)
Next
If folderDate.DayOfYear = DateTime.Today.DayOfYear
Else
System.IO.Directory.Delete(folder)
End If
Next
End Sub