In this work, the application of desirability function on controllability indices in the frequency domain is studied and a methodology is presented for its proper application. To design control structures, controllability indices are often used. Different indices represent different controllability attributes of the investigated system or systems; thus, their results might not be in agreement. With the desirability function, it is possible, however, to aggregate the different indices and a final ranking can be obtained, which may substitute time domain studies. Two different fields are examined: control structure variable pairing and selecting a distillation scheme that shows the best controllability features. On one hand, for the variable pairing step of the control structure design, the methodology does not deliver acceptable results, because controllability indices prove to be inaccurate in such cases on which the calculation is based. On the other hand, the methodology delivers similar result for the selection of the right distillation scheme from the controllability point of view to that of the load rejection investigations. This result shows the right area for the applicability of the methodology based on the desirability function.