It does not copy the source folder structure.

[ProgGiant]

When I convert a large number of music albums to mp3 for my phone, the folders are labeled with the artist name and album title, but the year of the album is not there, as it is in the source folder. This is important to me and I have to waste time comparing and editing the folder titles which is quite annoying and made me look for other software for this job. But I like this program and I will be happy if that changes.

[ralphldcm]

Did you set Options>General Setting>Output file to . Doing this I was able to copy my folder structure exactly. Otherwise freac seems to generate a new folder structure from scratch. By default it will include your entire folder structure added on to the output folder specified. I just created a new folder and moved the part of the directory I wanted to keep to that folder. However, if you use an option described in https://www.freac.org/manual/en/howto.html#anchor_pat , you can get just the part of the directory you want in the output folder. It makes use of the <directory+n(m)> format.
My problem with freac was that while it rips multi-artist cds and correctly sets albumartist to "various", when converting a folder from flac to ogg Vorbis, it set albumartist to the song artist and put each song is a separate folder, thus destroying the album structure.