Multi-beam scanning electron microscopy (MBSEM), has been developed to reduce the acquisition time by scanning multiple pixels simultaneously. The signal from the 14 × 14 beams is captured on a camera which reads out the position and intensity for each beam on the sample. But as we work with multiple beams and pixels we need a powerful technique for image acquisition and image processing algorithms. We use Field Programmable Gate Arrays (FPGA's), often used as an implementation platform for real time image acquisition and processing applications, because their structure is able to exploit spatial and temporal parallelism. This paper presents a technique for dealing with the various constraints of the camera and efficient mapping for image acquisition and processing operations on FPGA.