Several decades ago, the design of Physical Protection Systems (PPS) was typically done after a nuclear facility was completed. The evaluation of the PPS would occur using path analysis and tabletop exercises to identify deficiencies. Today, single analyst modeling and simulation tools dominate the field and allow for much more rapid and efficient design and analysis of a PPS. These tools also allow security requirements to be considered from the beginning of the facility design process in order to develop optimized and cost-effective protection strategies (Security by Design). The Material Protection, Accounting, and Control Technologies (MPACT) working group is demonstrating Safeguards and Security by Design (SSBD) for a generic electrochemical reprocessing facility as part of a 2020 Milestone. The Scribe3D© and PathTrace© tools have been used for PPS design and analysis to support this milestone. The PPS design process will be described along with the tools and analytical results. Security by Design recommendations are highlighted.