You can do a lot of things faster and easier using dos commands and batch files in Windows. If you want to move all files from a directory to another with subfolders, "robocopy" command is the easiest way to do it. To do this, you can use the following code:
robocopy C:\BaseDirectory D:\TargetDirectory *.* /E /XD D:\TargetDirectory /move
robocopyis included on windows7 and later systems by default. If you don't have robocopy on your system, you can try using xcopy command too.