The surface loss coefficients of CFx (x = 1 - 3) and F radicals have been measured on the stainless steel walls of the differential pumping systems of a plasma reactor. This measurement is made by comparing the beam to background signal ratio of the radicals measured by appearance potential mass spectrometry. The surface loss of the radicals in the differential pumping stages of the vacuum system, in addition to the pumping of the species due to the vacuum Dump, increases the beam to background signal ratio of the radical species. The measured loss coefficients are found to be lower than those reported on surfaces that have been exposed to fluorocarbon plasmas. This suggests that the loss coefficients of the species are dependent on the surface coverage of the radicals (CFx and F), which are lower on the walls in the differential pumping system. The measured loss coefficients in the differential pumping system are an order of magnitude lower than the loss coefficients measured in the afterglow of plasma chambers reported in the literature. We suggest the difference in the loss coefficients of radicals in the plasma chamber and those measured in this work are due to the differences in surface coverage in the two cases.