We present the results of a study of three-layered silicon biprismanes doped with methyl radicals and fluorine atoms by means of the density functional theory. Pentagonal, hexagonal, heptagonal, and octagonal doped systems were simulated in this study. We found that larger biprismanes demonstrate weaker interaction with dopants because they are less strained, and their surfaces are “flatter”. The weakening of interaction manifests itself by elongation of bond lengths between the silicon cage and the attached radicals. However, the energy gain / loss due to the reaction of substitutional doping is practically independent of the size of the system. The calculated partial Mulliken charges of fluorine atoms are about −0.3 of elementary charges. The corresponding value for methyl radicals is approximately three times smaller. HOMO-LUMO gaps of doped biprismanes demonstrate oscillations with increasing biprismane diameter with a general downward trend. The value of the gaps of the doped biprismanes is in the range from 2 to 3 eV and slightly differs from the gaps of the pristine biprismanes. The optical properties and excited states of doped biprismanes were calculated using the time-dependent density functional theory. Ultra-violet and visible spectra were determined for all considered systems. The absorption frequencies slightly depend on the radical type and the size of the system. However, the presence of radicals results in significant changes in the relative adsorption intensities of biprismanes with different shapes. We found that doping with methyl radicals and fluorine provided prevalent adsorption intensities of octagonal and hexagonal biprismanes, respectively. The observed effect can be used for optical detection of biprismanes with specific shapes or diameters in their mixture with other silicon structures.