Pulsed-radio frequency glow discharge optical emission spectrometry (Pulsed-RF-GDOES) has exhibited great potential for high resolution (HR) depth profiling. In this paper, the measured GDOES depth profile of 60 × Mo (3 nm)/B4C (0.3 nm)/Si (3.7 nm) was quantified by employing the newly extended Mixing-Roughness-Information depth (MRI) model. We evaluated the influences of the thickness and sputtering rate on the depth profile of very thin layers. We demonstrated that a method using the full width at half maximum (FWHM) value of the measured time-concentration profile for determining the sputtering rate and the corresponding thickness was not reliable if preferential sputtering took place upon depth profiling.