In this work, we explored the eigenspectra of minimally doubled fermions, in both Karsten-Wilczek and Borici-Creutz realizations. We generated 4-dim $SU(3)$ gauge fields with a definite topological
charge and calculated the chiralities of the eigenmodes for KW and BC fermions. We used the spectral flow of the eigenvalues for this purpose and demonstrated the Index theorem.