X-ray fluorescence (XRF) is a spectroscopic technique with applications in several fields, such as biology, food science and forensics. Often setups have multi-element detectors in order to improve the signal-to-noise ratio. The relative set of produced spectra have to be aligned to a reference spectrum, in a procedure that is referred to as energy calibration, which is necessary for the fitting. Automated methods fail and a manual procedure is typically employed instead. In this paper, we discuss the signal alignment problem of such systems and we illustrate the preliminary results of a new automated method for linear XRF spectra alignment, which potentially can be used also for other time-series like data.