Two-photon excitation using ultrashort laser pulses can selectively activate nanoparticles or excite fluorophores within thick biological samples. We show how the use of methods such as multiphoton intrapulse interference phase scan (MIIPS) to compensate phase distortions caused by microscope objectives with a high numerical aperture increases signal intensity and reproducibility in two-photon imaging. Using phase shaping of our compensated pulses, we demonstrate selective excitation of fluorophores within a mouse kidney sample, increasing the contrast between different subcellular structures compared to unshaped pulses.