In 2001, Scott joined Benetech as Senior Systems Administrator. He designed and implemented all non-Java code needed to run a Martus Server (including designing a novel high-security mode for running a Linux kernel, and developing an automated installation system usable by people with no Unix or GNU/Linux experience).  He ran most of the GNU/Linux servers for Martus.

Scott Weikart was Senior Systems Administrator based at Bengineering, the engineering department at Benetech, before transitioning to consultant.  He did much data processing of datasets used by HRDAG projects, with an emphasis on automated techniques to clean and canonicalize data, de-duplicate datasets, and link records between datasets.  He designed, built and ran Unix and GNU/Linux servers and storage systems for 25 years.