Dexterous continuum manipulators (DCMs) offer great potential for increasing instrument reach in minimally-invasive surgical procedures. We previously designed and fabricated a tendon driven DCM with a large instrument channel and evenly distributed compliant joints for minimally-invasive skull base surgery and the treatment of osteolysis during hip revision surgery. The evenly distributed compliant joints, in some cases, may limit the reach of the DCM during lesion removal. In this paper, we propose a finite element analysis (FEA) method for optimizing the distribution of the compliant joints based on treatment space requirements determined preoperatively. After performing experiments to validate the FEA results, we investigated the effects of height and cross distance of unevenly distributed compliant joints on tip trajectories and deflection shapes of DCMs. A boundary exploration for skull base surgery was performed to investigate the improvement in the percent of boundary explored by the optimized DCMs with the unevenly distributed compliant joints. Results show the advantage of using DCMs with unevenly distributed joints in reaching the boundary of the lesion. For a typical lesion in the petrous apex during skull base surgery, simulation results indicates that the design of unevenly distributed compliant joints can increase the reach of the DCM accomplishing 71% lesion removal compared with 59% from the DCM with evenly distributed compliant joints.