The fully propagated real time-dependent density functional theory method has been applied to study the laser-molecule interaction in 5- and 6-benzyluracil (5BU and 6BU). The molecular geometry optimization and the time-dependent electronic dynamics propagation were carried out using the M11-L local meta-NGA (nonseparable gradient approximations) exchange-correlation functional together with the def2-TZVP basis set. Different laser field parameters like direction, strength, and wavelength have been varied in order to estimate the conditions for an efficient excitation of the molecules. The results show that the two molecules respond differently to the applied laser field and therefore specific laser field parameters have to be chosen for each of them in order to get efficient and selective excitation behavior. It was also found that from the molecular excitation point of view not only the magnitude of the transition dipoles between the involved orbitals but also their orientation with respect to the laser field is important. On the other hand, it was shown that the molecular excitation is a very complex overlapping of different one-electron orbital depopulation-population processes of the occupied and virtual orbitals.