A multi-spot scanning technique using a spot array having a predetermined gap between spots can advantageously provide scalability to a large number of spots as well as the elimination of cross-talk between channels. The multi-spot scanning technique can select a number of spots for the spot array (1D or 2D), determine a separation between the spots to minimize crosstalk, and perform a scan on a wafer using the spot array and a full field of view (FOV). Performing the scan includes performing a plurality of scan line cycles, wherein each scan line cycle can fill in gaps left by previous scan line cycles. This “delay and fill” scan allows large spacing between spots, thereby eliminating cross-talk at the detector plane. In one embodiment, the scan is begun and ended outside a desired scan area on the wafer to ensure full scan coverage.