Suppressing fragmentation is a constant challenge in mass spectrometry because a molecular ion can readily be identified and provides information concerning the molecular weight of an analyte. Several techniques such as charge exchange chemical ionization (CECI) and vacuum ultraviolet emission ionization (VUVEI) have been developed to date for achieving this purpose. In this study, we report on the use of tunable ultraviolet (UV) and near-infrared (NIR) femtosecond (fs) lasers (35 fs) for the multiphoton ionization (MPI) of cis- and trans-4-methylcyclohexanols, the reference molecules that are currently used to examine fragmentation suppression. The results obtained here were compared with those obtained by CECI and VUVEI because they were reported as the best techniques for suppressing fragmentation. A molecular ion was strongly enhanced by carefully minimizing the excess energy in the ionic state using tunable UV and NIR fs-lasers. The ratio of the intensities for molecular and fragment ions, [M]+/[M-H2O]+, increased significantly (9.5-fold and 8.5-fold for cis- and trans-isomers, respectively, in UV fs-MPI) compared to the values obtained by CECI and VUVEI, respectively.