In the last four decades, computational techniques have become useful tools in liquid-phase enantioseparation for modeling analyte and chiral selector structures, as well as the mobile phase implicitly and explicitly, for exploring mechanisms underlying retention and enantioseparation, and for identifying noncovalent interactions that contribute to analyte-chiral selector binding and recognition. The present chapter briefly summarizes fundamentals and recent advances in the application of molecular modeling for understanding capillary electrophoresis enantioseparations promoted by cyclodextrin-based selectors. A practical example illustrates in detail the calculation and analysis of low-energy structures of single-isomer methylated cyclodextrins and their stereoelectronic properties.