The differences between three previously defined counterpoise (CP) schemes for removing the BSSE in molecular complexes formed by more than two subunits have been assessed by CP-corrected geometry optimizations and frequency calculations for the hydrogen fluoride trimer and tetramer. The types of the functional counterpoise (FC) procedures included the site–site (SSFC), pairwise additive, and hierarchical Valiron–Mayer (VMFC) schemes. The latter approach takes into account the basis set extension of the dimers in the trimer, dimers and trimers in the tetramer, etc. The number of different calculations required to apply this counterpoise scheme increases very rapidly with the cluster size. The symmetry of the chosen systems makes the test of this approach computationally feasible. All the optimizations and frequency calculations have been carried out automatically using a new program that generates the necessary input files and repeatedly calls a slightly modified version of a Gaussian link. The results show that geometrical parameters, zero-point vibrational energies, and redshifts computed on the CP-corrected potential energy surfaces differ considerably from those evaluated on the uncorrected surfaces. The structural and energetic properties obtained with the conventional SSFC procedure are almost identical to those predicted by the more costly and complex VMFC method. Hence, the former seems to be more appropriate in the present case. Furthermore, symmetry-adapted perturbation theory calculations show the importance of computing the interaction energies at the CP-corrected geometries.