The lack of detailed experimental controls has been one of the major obstacles that hinder the progress in molecular electronics. While experimental data remains all over the map, specific details, related mechanisms, and data analysis techniques are in high demand to promote our physical understanding at the single-molecule level. A series of modulations we recently developed based on traditional scanning probe microscopy break junction (SPMBJ) have helped to discover significant detailed properties hidden in the contact interfaces of a SMBJ, For example, in the past we have shown that the correlated force and conductance changes under the saw tooth modulation and stretch-hold mode of PZT movement revealed inherent differences in contact geometries of a molecular junction. In this paper, using bias modulated SPMBJ and utilized emerging data analysis techniques, we report on the measurements of altered alignment of the HOMO of benzene molecules when we changed the anchoring group which coupled the molecule to metal electrodes. Further calculations based on Landauer fitting and transition voltage spectroscopy (TVS) demonstrated the effects of modulated bias on the location of the frontier molecular orbitals. Understanding the alignment of the molecular orbitals with the Fermi level of the electrodes is essential for understanding the behaviour of SMBJs and for the future design of more complex devices. With these modulations and analysis techniques, fruitful information has been found about the nature of the metal-molecule junction， providing us insightful clues for the next step for in-depth study.