A deformable registration method is proposed to register a brain atlas with tumor-bearing brain scans. The tumor mass effect is first simulated in the (normal) atlas, using a biomechanical model of mass effect. The tumor-bearing atlas is subsequently warped to the patient's scan by a deformable registration method, built upon the idea of HAMMER registration algorithm developed for normal brains. The potential of using the pattern of deformation around the tumor region to optimize the location of tumor seed and other parameters of the tumor model is also explored. Quantitative evaluation on simulated data shows that the proposed method achieves accuracy similar to that achieved in registration of images without tumors. Moreover, limited registration results on real tumors are promising.