The time-dependent optical properties of molecular systems are investigated by step-scan Fourier-transform spectroscopy in order to explore the dynamics at phase transitions and molecular orientation in the milli- and microsecond range. The electrical switching of liquid crystals traced by vibrational spectroscopy reveals a rotation of the molecules with a relaxation time of 2 ms. The photo-induced neutral-ionic transition in TTF-CA takes place by a suppression of the dimerization in the ionic phase and creation of neutral domains. The time-dependent infrared spectra depend on temperature and laser pulse intensity; the relaxation of the spectra follows a stretched-exponential decay with relaxation times in the microsecond range strongly dependent on temperature and laser intensity. We present all details of the experimental setups and thoroughly discuss the technical challenges.