Biological imaging for isolation and concentration of pathogen or sub-micron particle is an emerging field covering a wide range of applications critical to biological and clinical research. A variety of these applications often require isolation of rare cells or diluted pathogens from large volumes (few ml) of complex biological samples. Isolation of pathogens using active electrophoresis involving microarrays enables volume-level transport, accumulation, and hence separation of pathogens and cells. In conventional microarrays, the electric field away from planar electrodes decays rapidly, resulting in an inability to collect and isolate samples effectively. Hence for biological applications involving high-volume manipulation, microarrays with 3-dimensional electrodes provide an efficient solution. The use of 3-D microarrays with carbon electrodes for isolation of DNA offers wider range of manipulating voltage for large volume samples. To analyze the efficiency of accumulation in 3-D microarrays, electrophoretic experiments are carried out by manipulating the polystyrene beads (which mimic the DNA) in a high-efficiency, high-volume 3-D C-MEMS fabricated biochip using closed-cell electrophoresis. Experiments are captured with a CCD camera and 2-D image processing is carried out using Matlab. Individual Regions of Interest (ROI) were created on a biochip and examined using the multi-location capability of Matlab. This allowed the description of beads' (i) dynamic distribution of beads, (ii) movement of beads from one electrode to another electrode when biased, (iii) accumulation (before and after biasing), and (iv) repulsion (before and after biasing). Algorithms were developed to measure the performance of a biochip for comparing the efficiencies of various ROIs in and around positively and negatively charged electrodes. Further 3-D Image Analysis is conducted for demonstrating the ability of the 3-D electrode to accumulate beads along its height (Z-axis) using Scanning Electron Microscopy and Hirox digital microscopy followed by the quantification of percentage accumulation using Keyence digital microscopy. The results of quantification suggest that in 3-D microarrays, the concentration of accumulation at the electrodes increases 10 folds from initial concentration. Further the analysis on 2-D metal vs. 3-D carbon electrodes establish that there is higher rate of accumulation with 3-D carbon electrodes and hence establishes a critical proof that 3-D carbon electrode microarrays could enable high collection efficiency biochips.