We developed an improved method for tilt series alignment with fiducial markers in electron tomography. Based on previous works regarding alignment, we adapted the Levenberg-Marquardt method to solve the nonlinear least squares problem by incorporating a new formula for the alignment model. We also suggested a new method to estimate the initial value for inversion with higher accuracy. The proposed approach was applied to geopolymers. A better alignment of the tilt series was achieved than that by IMOD S/W. The initial value estimation provided both stability and a good rate of convergence since the new method uses all marker positions, including those partly covering the tilt images.