Modern cell sorters and the more sophisticated variety of analytical flow cytometers allow for analysis of multiple fluorochromes and, consequently, for optical configuration changes by the user. The problem faced is that as more fluorochromes are simultaneously employed in flow cytometric analyses, so do their emission spectra crowd more closely together and increasingly overlap. It then becomes even less acceptable to consider only the peak wavelength of each emission in selecting an appropriate optical filter. Further, given the limited collection of exciting laser wavelengths, it is unrealistic to require close proximity of these wavelengths to the respective peaks of the excitation spectra. More recently, graphical methods have been introduced to better display the match between emission spectrum and optical filter transmission and between exciting laser and excitation spectrum. In this paper, a more analytical method is proposed in which a computer program outputs numerical data for the key measures of suitability of a proposed configuration. These are the degree of transmission of a fluorochrome through the filter designated for it, the degree of spillover into other optical filters in the system, the relative efficiency of excitation of each fluorochrome by the available laser lines and the degree of leakage of each optical filter for each of the laser lines used. The program has been implemented as a Java applet called FCMDesigner that can be displayed for public access on a web site.