The National Transportation Security Center of Excellence (NTSCOE) was established in August 2007 to develop new approaches to defend, protect, and increase the resilience of the nation’s multi-modal transportation infrastructure, and to create education and training programs for transportation security. The Center for Transportation Safety, Security, and Risk (CTSSR) at Rutgers University, an NTSCOE institution, developed models that address multi-modal resilience of freight and transit transportation networks. Data collection processes for each project presented significant hurdles for the research team in developing credible and accurate modeling tools. For any given data need, the potential exists for data gaps, collection, and processing errors, publication and use restrictions, and the need to obtain the most timely information. These challenges must be foreseen by researchers and practitioners in order to better accommodate potential restrictions on both data collection and dissemination while still providing users with a tool that improves decision making.