Flanagan currently operates his own company, Den's Design Studio, which has supplied puppets, costumes, and specialty props for Saturday Night Live and Last Week Tonight with John Oliver (including Sesame-style puppets on the latter). He has also worked extensively on stage productions, including puppets and props(including the Time Dragon and the lion cub) for the Broadway production of Wicked and puppet and mask designs for off-Broadway shows Beowulf, The Hairy Beast and The Emperor Jones (earning a Drama Desk Award nomination for Outstanding Costume Design for the latter).