It is currently not possible to deconstruct raft bases. When attempting to deconstruct bases players will receive an error message saying the object still supports other items and cannot be destroyed.
Update: This issue may not affect every player, some players may find they can deconstruct bases without issue. If you have found this to be an issue however, please let us know.
There is currently no workaround for this issue. However, it may be possible to break down raft bases if only one side is attached to something else.