A high throughput deposition apparatus includes a process chamber, a plurality of targets that form a first closed loop in the process chamber, wherein the first closed loop includes a long dimension defined by at least a first pair of targets and a short dimension defined by at least a second pair of targets, a first substrate carrier assembly that can hold one or more substrates and configured to receive a deposition material from the plurality of targets in the first closed loop, and a transport mechanism that can move the first substrate carrier assembly along an axial direction through the first closed loop in the first process chamber.