Methods and apparatuses are provided that determine an offset between actual feature/mark locations and the designed feature/mark locations in a maskless lithography system. For example, in one embodiment, a method is provided that includes opening a camera shutter in a maskless lithography system. Light is directed from a configuration of non-adjacent mirrors in a mirror array towards a first substrate layer. An image of the first substrate layer on a camera is captured and accumulated. Light is directed and images are captured repeatedly using different configurations of non-adjacent mirrors to cover an entire field-of-view (FOV) of the camera on the first substrate layer. Thereafter, the camera shutter is closed and the accumulated image is stored in memory.