Microscopic images are quite helpful for us to observe the details of cells because of its high resolution. Furthermore it can benefit biologists and doctors to view the cell structure from any aspect by using a serial images to generate 3D cell structure. However each cell slice is placed at the microscopy respectively, which will bring in the arbitrary rotation and translation among the serial slices. What's more, the sectioning process will destroy the cell structure such as tearing or warping. Therefore we must register the serial slices before rendering the volume data in 3D. In this paper we propose a robust registration algorithm based on an improved 3D Hilbert scam search. Besides we put forward a simple but effective method to remove false matching in consecutive images. Finally we correct the local deformation based on optical-flow theory and adopt multi-resolution method. Our algorithm is tested, on a serial microscopy kidney cell images, and the experimental results show how accurate and robust of our method is.