On my system (Ubuntu Linux) with SBT 0.13.5 and some projects from the Coursera Functional Programming course I found the folders all totalled up to 2.1GB for 12 projects due to all the cache files and duplicated Scala downloads.
The current SBT commands that work and get almost everything cleaned is:
sbt clean clean-files
This removes the top level "target" and "lib_managed" folders (23MB down to 3.2MB in this case) but leaves some target folders under project:
./project/project/project/target
./project/project/target
./project/target
This is where the Linux find command (also posted by @jack-oconnor) is very helpful:
find . -name target -type d -exec rm -rf {} \;
This gets us back down to a mere 444KB for one of my own projects and the 2.1GB goes down to 5.0MB !
In windows you won't have as many useful command line options, e.g. no star wildcards in path names, but you can always try and force it with:
rmdir /s /q target project/target project/project/target
The best I can do on automatically finding is a DIR command:
dir /ad /s /b | find "target"