If your files are located as you say (that is, D:\Flac\Artist\Album), then the Fill Properties From Filename will work fine. This is a standard use case.
Set to Template mode, and fill the following templates:
Directories:
D:\Flac\[Artist]\[Album]\
Filename:
[Name]
(you don't indicate if your song file names contain Track #, but if they did, the Filename template will be something like:
Filename:
[Track #] [Name]
It really is quite trivial matching, so I'm sure you'll have no trouble getting it to work.