Optimal control of rovibrational excitations of the CO molecule using picosecond infrared laser pulses is described in the framework of the electric-nuclear Born-Oppenheimer approximation [G. G. Balint-Kurti et al., J. Chem. Phys. 122, 084110 (2005)]. The potential energy surface of the CO molecule in the presence of an electric field is calculated using coupled cluster theory with a large orbital basis set. The quantum dynamics of the process is treated using a full three dimensional treatment of the molecule in the laser field. The detailed mechanisms leading to efficient control of the selected excitation processes are discussed.