This article systematically analyzes all possible operation modes in a two lens focused ion beam column utilizing analytical formalism and numerical analysis. The non-crossover mode is found to be inherently superior to the crossover mode, and a column in the crossover mode with a single fixed aperture can never realize optimal magnifications for all beam current levels. The non-crossover mode gives the best resolution. The crossover mode, however, offers many attractive features such as simplicity and quick changeover time. Optimization procedures based on operational mode analysis with examples are also given.