Adaptive optics, beam-shaping, wavefront correction, or modification with spatial light modulators (SLMs) has been done for many years. Most of the systems used in these techniques control the change in the wavefront by using a wavefront sensor placed in a plane optically conjugated with the SLM. We present a method, specially developed for these kinds of systems, for easily aligning the phase projected on the SLM. The method is based on the minimization of the undesired Zernike coefficients generated when the phase element projected in the SLM is displaced or rotated with respect to the reference frame of the optical system. Owing to the proposed method, we were able to detect and correct a rotation of the SLM of 1.42 deg and center the projected phase with a precision equal to the size of the pixel of the SLM (8  μm in our experiment).