This document provides an in-depth description of the role of the LSST Project in preparing software and providing computational resources to process the data from Special Programs (deep drilling fields and/or mini-surveys). The plans and description in this document flow down from the requirements in LSE-61 regarding processing for Special Programs. The main target audience is the LSST Data Management (DM) team, but members of the community who are preparing white papers on science-driven observing strategies may also find this document useful. The potential diversity of data from Special Programs is summarized, including boundaries imposed by technical limitations of the LSST hardware. The capability of the planned Data Management system to processes this diversity of Special Programs data is the main focus of this document. Case studies are provided as examples of how the LSST software and/or user-generated pipelines may be combined to process the data from Special Programs.