We have developed a system model using the System Modeling Language (SysML) for the Alignment and Phasing System (APS) on the Thirty Meter Telescope (TMT). APS is a Shack-Hartmann wave-front sensor that will be used to measure the alignment and phasing of the primary mirror segments, and the alignment of the secondary and tertiary mirrors. The APS system model contains the ow-down of the Level 1 TMT requirements to APS (Level 2) requirements, and from there to the APS sub-systems (Level 3) requirements. The model also contains the operating modes and scenarios for various activities, such as maintenance alignment, post-segment exchange alignment, and calibration activities. The requirements ow-down is captured in SysML requirements diagrams, and we describe the process of maintaining the DOORS database as the single-source-of-truth for requirements, while using the SysML model to capture the logic and notes associated with the ow-down. We also use the system model to capture any needed communications from APS to other TMT systems, and between the APS sub-systems. The operations are modeled using SysML activity diagrams, and will be used to specify the APS interface documents. The modeling tool can simulate the top level activities to produce sequence diagrams, which contain all the communications between the system and subsystem needed for that activity. By adding time estimates for the lowest level APS activities, a robust estimate for the total time on-sky that APS requires to align and phase the telescope can be obtained. This estimate will be used to verify that the time APS requires on-sky meets the Level 1 TMT requirements.