The Cherenkov Telescope Array (CTA), with more than 100 telescopes, will be the largest ever ground-based gamma-ray observatory and is expected to greatly improve on both gamma-ray detection sensitivity and energy coverage compared to current-generation detectors. The 9.7-m Schwarzschild-Couder telescope (SCT) is one of the two candidates for the medium size telescope (MST) design for CTA. The novel aplanatic dual-mirror SCT design offers a wide field-of-view with a compact plate scale, allowing for a large number of camera pixels that improves the angular resolution and reduce the night sky background noise per pixel compared to the traditional single-mirror Davies-Cotton (DC) design of ground-based gamma-ray telescopes. The production, installation, and the alignment of the segmented aspherical mirrors are the main challenges for the realization of the SCT optical system. In this contribution, we report on the commissioning status, the alignment procedures, and initial alignment results during the initial commissioning phase of the optical system of the prototype SCT.