The primary, secondary and tertiary mirrors of the Thirty Meter Telescope (TMT), taken together, have approximately 12,000 degrees of freedom in optical alignment. The Alignment and Phasing System (APS) will use starlight and a variety of Shack-Hartmann based measurement techniques to position the segment pistons, tips, and tilts, segment figures, secondary rigid body motion, secondary figure and the tertiary figure to correctly align the TMT. We present a conceptual design of the APS including the requirements, alignment modes, predicted performance, software architecture, and an optical design.