Be stars are found to rotate close to their critical rotation and therefore they are considered as an important laboratory of study for stellar rotation. In this context, we obtain the projected rotational velocity of a sample of classical Be Southern stars in the BeSOS database via Fourier Transform in an automated way for several absorption lines at different epochs. A Gaussian profile is fitted to eight observed photospheric He lines in order to select automatically the spectral signal given by areas under the curve of 95.45 %, 98.75 % and 99.83 % from the profile to obtain 𝑣 sin 𝑖 via Fourier Transform technique. The values obtained are in global agreement with the literature. Analysing only one line is not enough to set the 𝑣 sin 𝑖 value, depending on the line the value in most cases are underestimated with respect to 𝜆4471. When gravity darkening effects are including, apparent values increases by ∼ 10 %. The resolution of the instrument PUCHEROS used for BeSOS spectra (𝑅 ∼ 17 000) constrain a theoretical lower bound possible at 𝑣 sin 𝑖 ∼ 100 km s −1 . The procedure has limitations using a linear limb-darkening function with 𝜀 = 0.6 for classical Be stars rotating close to the break-up velocity without gravity-darkening corrections, which can't be negligible. Previous works measure 𝑣 sin 𝑖 values using just one spectral line and here we demonstrate that with more lines the results can varies. This could be due to the photospheric distribution of atomic transitions on classical Be stars.