This paper performs a numerical study of the imaging process in confocal microscopy. We simulate the imaging result using Fresnel diffraction formula. We also consider the divided aperture technique in confocal system. Different aperture shapes were varied to achieve best performance in terms of resolution and integrated intensity. Here, the D-shaped achieves the best performance in x-axis resolution, while the annular aperture shape is the worst for integrated intensity. We propose using different aperture shapes for various biomedical applications.