We study specific properties of different isotopes by applying optimal control. Selective optimization for 23Na39K and 23Na41K isotopes is reported at two different central wavelengths by employing evolutionary strategies on shaped femtosecond laser pulses. The optimized ionization processes exhibit high enhancements of one isotope compared to the other and reversed. We analyze the pulse spectra for extracting information about the optimally chosen ionization paths and observe vibrational transitions to differing electronic states for the different isotope selections. To get a deeper insight we compare simultaneous phase and amplitude modulation with pure amplitude modulation and as well pure phase modulation. Our approach reveals how the optimization algorithm precisely addresses the vibrational wave functions by coherent interaction with the corresponding pulse components.