We proposed a target-based cone beam computed tomography (CBCT) imaging framework in order to optimize a free three dimensional (3D) source-detector trajectory by incorporating prior 3D image data. We aim to enable CBCT systems to provide topical information about a region of interest (ROI) using a short-scan trajectory with a reduced number of projections. The best projection views are selected by maximizing an objective function fed by the image quality by means of applying different x-ray positions on the digital phantom data. Finally, an optimized trajectory is selected which is applied to a C-arm device able to perform general source-detector positioning. An Alderson-Rando head phantom is used in order to investigate the performance of the proposed framework. Our experiments showed that the optimized trajectory could achieve a comparable image quality in the ROI with respect to the reference C-arm CBCT while using approximately one-quarter of projections. An angular range of 156° was used for the optimized trajectory.