Combination of micro Positron Emission Tomography with micro Computed Tomography (microPET/micro-CT) has been widely used in clinical and scientific research. Multimodality of microPET/micro-CT makes it a representative hybrid imaging device. However, its high prices hampered its widespread use. Previous work was concentrated on achieving complicated process of fusion images manually. Registration problem is a prerequisite for image fusion. Therefore, an effective method for accurate image registration between stand-alone micro-PET and micro-CT scanners is needed. Presented work proposes a multimodal images using separate micro-PET and microCT devices as well as implements a registration method by combining hardware and software. An animal chamber was designed which can be mounted on micro-PET and micro-CT scanners separately. Four catheters filled with (18)F2-deoxy-2-fluoro-D-glucose (F-18-FDG) solution were used to generate the spatial relation between PET and CT images. The transformed matrix was calculated during each registration experiment instead of a predetermined one, which decreased errors introduced by uncertainty in the position of animal chamber. In this way multi-modality biomedical images are acquired automatically without human intervention. These in vivo and test experimental results show the accuracy of this method. As stated above, this method is effective and robust for multi-modality image fusion.