Measurements of two-photon absorption (TPA) cross sections are greatly confounded by even very weak linear absorption, for example from hot bands. In this case, the experimental power dependence of fluorescence from amplified and mode-locked laser systems can differ drastically, even if the peak intensity is adjusted to be the same in both cases. A simple pulse train shaping method suppresses linear contributions and extracts the nonlinear absorption cross section, demonstrated here for a meso-to-meso ethyne-bridged bis[(porphinato)zinc(II)] fluorophore (DD) at 800 nm. This approach permits reliable TPA cross-section measurement, even with standard modelocked lasers under conditions identical to that used for multiphoton microscopy.