The control structure design is an important step of process synthesis. This activity can be supported with controllability indices of the process to be designed. Existing methods to calculate these indices are very complicated and time consuming. In this article, a methodology is presented for the simple determination of controllability indices in the frequency domain. With this methodology, the process of making open loop simulations to approximate transfer function matrices can be avoided. The results obtained can be used to evaluate different control structures. The methodology uses the Control Design Interface module of Aspen Dynamics to describe the system with the linear state space representation. The state space representation can be transferred into Matlab that is used to calculate the controllability indices in the function of frequency from the matrices transferred. The methodology is introduced on two thermally coupled distillation systems (side-stream stripper, SS, and side-stream rectifier, SR). The results show that the methodology is well applicable. The SS has better controllability properties than the SR if the BC separation is easier than AB. In the other cases the SR is better.