Using instanton effects, we discuss the problem of fermion mass hierarchies in an MSSM-like Type IIA orientifolded model with U(3) × Sp(1) × U(1) × U(1) gauge symmetry obtained from intersecting D6-branes. In the corresponding four-stack quiver, the different scales of the generated superpotential couplings offer a partial solution to fermion mass hierarchies. Using the known data with neutrino masses τ < ∼ 2 eV, we give the magnitudes of the relevant scales.