The Atacama Cosmology Telescope (ACT) is designed to measure temperature anisotropies of the cosmic microwave background (CMB) at arcminute resolution. It is the first CMB experiment to employ a 32×32 closepacked array of free-space-coupled transition-edge superconducting bolometers. We describe the organization of the telescope systems and software for autonomous, scheduled operations. When paired with real-time data streaming and display, we are able to operate the telescope at the remote site in the Chilean Altiplano via the Internet from North America. The telescope had a data rate of 70 GB/day in the 2007 season, and the 2008 upgrade to three arrays will bring this to 210 GB/day.