A theoretical description to calculate transient absorption spectra of photoreactive systems in the condensed phase is developed. The formulation comprises a multidimensional model of nonadiabatic photoisomerization, a Redfield treatment of the environment within the secular approximation, and a doorway-window formulation to calculate transient pump-probe spectra. Employing the eigenstate representation and assuming Gaussian laser pulses, we derive explicit expressions for the doorway and window operators. The formalism scales with N-2 (N being the dimension of the system Hamiltonian matrix) and therefore allows us to handle multidimensional molecular models. Detailed computational studies of the dynamics and transient absorption are presented for various cis-trans photoisomerization models. It is shown that only the two-mode model involving a conical intersection yields short-time transients, as expected for a condensed-phase system. Problems in the interpretation of transient spectra associated with the competition (and cancellation) of the various spectroscopic contributions in a photoreaction are discussed in some detail. The computational studies demonstrate the need for theoretical modeling in order to achieve a microscopic interpretation of femtosecond experiments.