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We designed and built a unique instrument that combines a two-photon laser scanning microscope (LSM) with an inverted atomic force microscope (AFM). Local photoluminescence (PL) spectroscopy and three-dimensional lithography are demonstrated using the two-photon LSM. High spatial resolution topographic images from the AFM can be recorded simultaneously with the PL images of the same region, allowing us to correlate PL variation and surface features of the sample. The wavelength of the short-pulse laser excitation can be varied continuously from 700 to 800 nm while the detection setup is optimized for signals between 350 and 650 nm. We demonstrate the performance of this instrument by examining the spatial variation of PL signals in GaN samples and by fabricating photonic crystal structures in polymer films. © 2003 American Institute of Physics.