We analyze the alignment of the low multipoles (quadrupole and octupole) of various maps of the WMAP 5yr release: the CMB maps obtained with ILC and MCMC methods, the CMB map in the V band after foreground reduction, and, for comparison, the (not cleaned) V band map. We study how much this alignment is polluted by residuals on the Galactic region. Among the considered maps, the WMAP-ILC turns out to be the most clean map from the point of view of the proposed test. This result has been found studying the redistribution (due to the masking process) of each bin of the probability distribution functions of the alignment estimators. By construction, our method, feasible through Monte Carlo simulations, works for any possible mask adopted in the analysis of data from current and forthcoming CMB anisotropy experiments and it can only exclude that the considered map is clean.