The Soreq Applied Research Accelerator Facility (SARAF) is a 5-40 MeV, 0.04-2 mA proton/deuteron RF superconducting linear accelerator. National Instruments (NI) Hardware and Software has been selected as a framework for the SARAF Main Accelerator Control System (MACS). Examples of chosen NI Software are Real-Time (RT) and Datalogging and Supervisory Control (DSC) including Citadel Database. This paper describes the design and implementation of the SARAF Control System based on NI Hardware and Software. We emphasize the problems which arose during commissioning and present our solutions.