The molecular weight of target compounds in many organic syntheses in the pharmaceutical industry is in the range of 300-1000 Da. Separation processes based on organic solvent-resistant nanofiltration membranes are being explored to separate these valuable products from the smaller molecular weight products and residual reactants present in the reaction mixture. Through numerical modeling and use of realistic values for the parameters in organic syntheses involving compounds of diverse molecular weights and hence, diverse sizes, this study shows that the production of the target compound can be enhanced significantly using nanofiltration. Enhancement is examined from the perspectives of conversion (yield), reduction of reaction time, selectivity and potential elimination of subsequent downstream separation steps.