We employ Minkowski functionals to analyze the kinetics of pattern formation under an applied external shear flow. The considered pattern formation model describes the dynamics of phase separating block copolymer systems. For our purpose, we have chosen two block copolymer systems (a melt and a solution) that exhibit a hexagonal cylindrical morphology as an equilibrium structure. Our main objective is the determination of efficient choices for the treshold values that are required for the calculation of the Minkowski functionals. We find that a minimal set of two treshold values (one from which should be equal to an average density value and another to a higher density value) is sufficient to unraffle the phase separation kinetics. Given these choices, we focus on the influence of the degree of phase separation, and the instance at which the shear is applied, on the kinetic pathways. We also found a remarkable similarity of the time evolution of Euler characteristic and the segregation parameter for the average density choice. (C) 2004 American Institute of Physics.