We present a 2D to 3D registration framework that compensates for prostate motion and deformations during freehand prostate biopsies. It has two major components: 1) a trajectory-based rigid registration to account for gross motions of the prostate; and 2) a non-rigid registration constrained by a finite element model (FEM) to adjust for residual motion and deformations. For the rigid alignment, we constrain the ultrasound probe tip in the live 2D imaging plane to the tracked trajectory from the pre-procedure 3D ultrasound volume. This ensures the rectal wall approximately coincides between the images. We then apply a FEM-based technique to deform the volume based on image intensities. We validate the proposed framework on 10 prostate biopsy patients, demonstrating a mean target registration error (TRE) of 4.63 mm and 3.15 mm for rigid and FEM-based components, respectively.