An overlay metrology system comprising: a controller communicatively coupled to a telecentric imaging system including two or more cameras configured to capture images through an objective lens at two or more focal positions, the controller including one or more processors configured to execute program instructions causing the one or more processors to: receive two or more alignment images of an overlay target on a sample captured at two or more focal positions by the imaging system, the two or more alignment images including one or more features of the overlay target; generate alignment data indicative of an alignment of the overlay target within the imaging system based on the two or more alignment images; set the two or more alignment images as measurement images when the alignment of the overlay target is within selected alignment tolerances; direct the imaging system to adjust the alignment of the overlay target in the imaging system and further receive one or more measurement images from the imaging system when the alignment of the overlay target is outside the selected alignment tolerances; and determine overlay between two or more layers of the sample based on at least one of the measurement images; wherein the two or more cameras are configured to image two or more different focal positions, wherein one of the cameras is configured to image at a nominal focal position at which the overlay target is expected to be aligned and the one or more other cameras (302b; 302c) are configured to image at selected offsets from the nominal focal position, wherein the two or more cameras simultaneously generate the two or more alignment images. a controller communicatively coupled to a telecentric imaging system including two or more cameras configured to capture images through an objective lens at two or more focal positions, the controller including one or more processors configured to execute program instructions causing the one or more processors to: receive two or more alignment images of an overlay target on a sample captured at two or more focal positions by the imaging system, the two or more alignment images including one or more features of the overlay target; generate alignment data indicative of an alignment of the overlay target within the imaging system based on the two or more alignment images; set the two or more alignment images as measurement images when the alignment of the overlay target is within selected alignment tolerances; direct the imaging system to adjust the alignment of the overlay target in the imaging system and further receive one or more measurement images from the imaging system when the alignment of the overlay target is outside the selected alignment tolerances; and determine overlay between two or more layers of the sample based on at least one of the measurement images; receive two or more alignment images of an overlay target on a sample captured at two or more focal positions by the imaging system, the two or more alignment images including one or more features of the overlay target; generate alignment data indicative of an alignment of the overlay target within the imaging system based on the two or more alignment images; set the two or more alignment images as measurement images when the alignment of the overlay target is within selected alignment tolerances; direct the imaging system to adjust the alignment of the overlay target in the imaging system and further receive one or more measurement images from the imaging system when the alignment of the overlay target is outside the selected alignment tolerances; and determine overlay between two or more layers of the sample based on at least one of the measurement images;