You can use robocopy for this. E.g. in PowerShell (all one one line as single command):
Code:
PS C:\Users\Username> robocopy "C:\Users\Username\Documents" "D:\EmptyFileLocation" -s -create
-s makes robocopy recursively add subdirectories, omitting empty ones
-e would do the same, except it includes empty subdirectories
-create creates zero-length files instead of copying existing ones