Gaseous fluorine-containing molecules are crucial for controlled etching in semiconductor industries. This work presents the first-principle density functional theory (DFT) study on the modification of silicon nitride surface by fluorine-containing gases such as HF, CF4, CHF3, CH2F2, and CH3F. The reactions were modeled and simulated by assuming that the silicon nitride surface was exposed to a single fluorine-containing molecule to form different resulting surface groups and byproducts. For all fluorine-containing molecules, the SiF* formation was expected to be spontaneous. For the CHxF4−x (x = 0 to 3) molecules, the formation of SiNHCHxF3−x* was also predicted as an exothermic reaction. In the case of CH3F only, the activation energy (EA) for the SiF* formation was 0.98 eV, which is significantly lower than 2.03 eV for the SiNHCH3* formation. For the other CHxF4−x molecules, the activation energies for the formation of SiNHCHxF3−x* and SiF* were approximately the same. For the SiF* formation, CH3F showed the lowest EA value on the silicon nitride surface, whereas HF showed the lowest EA value on the silicon oxide surface. The selective fluorination of silicon nitride with CH3F was explained using the absence of fluorine in the CH3 after the dissociation of a fluorine atom and the basicity of the silicon nitride surface. These findings imply that with a good selection of a fluorine-containing gas, SiF* can be selectively produced on a specific surface.