# find . -depth -mindepth 1 -maxdepth 3 -type d -exec rmdir {} \;

This finds directories, between 1 and 3 levels deep and attempts to remove them. The -depth flag finds the deepest child directories, before finding parents. This is great, because it tries to remove foo/bar/ before it will try to remove foo/. Without removing foo/bar/ first, rmdir foo/ would fail. Because rmdir will fail if there are any contents in a directory, the operation is safe to run without removing any files. You could redirect STDERR to a file, and capture all the directories that are not empty for processing later.