In the present work the influence of a non-ideal separation step of a supercritical fluid extraction (SFE) unit was studied; the solvent used was carbon dioxide. The behavior of clove bud (Eugenia caryophyllus), vetiver grass (Vetiveria zizanioides), and fennel (Foeniculum vulgare) was analyzed. The starting point was a previous study on the same subject, which considered that no solute is lost in the vapor phase and a fixed fraction of 2% of the CO2 is lost within the heavy phase. The flash separation step was simulated using the SuperPro Designs 6.0® Software, which calculates the phase equilibrium that occurs during the separation step using the Peng–Robinson equation of state. Experimental data for extraction kinetics from vetiver grass were obtained at 313 K and 20 MPa. Phase equilibria for CO2/vetiver extract were measured at pressures from 7.5 to 30 MPa and temperatures of 303.2, 318.2 and 333.2 K; CO2 weight fraction varied from 0.1 to 0.99. The flash tank experimental data was obtained for fennel at 4 MPa and 293 K; the resulting anethole loss was 1.45%. The costs of manufacturing (COM) of the SFE extracts were determined according to Turton et al. using Tecanalysis v 1.0; the influence of the non-ideal flash separation step on COM was studied for clove buds.